Things in the game that really made no sense.

[doc7924]

Bus stops with no buses

Having destructive super powers like AOEs and novas and ONLY hitting the bad guys even though your teammates are standing right next to you

Running at super speed through the streets only to be stopped cold by a mail box or the bus-less bus stops

Little old ladies being able to hang onto their purses being pulled by mobs for days on end without ever stopping

[Blackout]

Bus stops with no buses

Having destructive super powers like AOEs and novas and ONLY hitting the bad guys even though your teammates are standing right next to you

Running at super speed through the streets only to be stopped cold by a mail box or the bus-less bus stops

Little old ladies being able to hang onto their purses being pulled by mobs for days on end without ever stopping

Well, clearly those little old ladies are either Nemesis automatons, or heroes who don't want to blow their secret identities by fighting back.
Also a few other one's; The Clockwork working, Malta using anything other than sappers, Sky raiders using anything other than jet-packs and force-fields, and Lord Recluse relying entirely on shrimp to fuel the Rogue Isles economy 

[blacksly]

Well, clearly those little old ladies are either Nemesis automatons, or heroes who don't want to blow their secret identities by fighting back.
Also a few other one's; The Clockwork working, Malta using anything other than sappers, Sky raiders using anything other than jet-packs and force-fields, and Lord Recluse relying entirely on shrimp to fuel the Rogue Isles economy 

Those aren't all shrimp... half of those "shrimp" fishermen are actually black market smugglers.
That's why the Rogue Isles are such a wretched hive of scum and villainy.

[Paragon Avenger]

In Issue 23, the trainers being tailors.  There you are standing in board daylight having your costume altered.

How about being in a large room with about 8 mobs.  You fight one mob using noisy powers, and the other mobs just stand their ground pounding their fists into their hands.  Even if they can't hear you, they can see you.

[The Fifth Horseman]

Also a few other one's; The Clockwork working,

Eh, the Clockwork were pretty much outright said to be puppets animated by Clockwork King's psychic powers.

[Aggelakis]

Eh, the Clockwork were pretty much outright said to be puppets animated by Clockwork King's psychic powers.

Yep. That's why psychic type did so much more damage to them!

[MaidMercury]

I once followed a few pedestrians just to see the walk algorithm.

It was a mindless long circle around buildings, sometimes going up stairs (Train station).
...then down again leading to no real destination.

[Vee]

It was a mindless long circle around buildings, sometimes going up stairs (Train station).
...then down again leading to no real destination.

So pretty much just like real life then?

[Floride]

A cow mooing in the ski chalet
Lakes that are only 2 feet deep
Police in a city full of thousands of super-powered heroes
Universities with no classrooms or lecture halls

and my absolute favorite...

The handicap parking space for King's Row PD is the FARTHEST space from the door

[doc7924]

In Issue 23, the trainers being tailors.  There you are standing in board daylight having your costume altered.

How about being in a large room with about 8 mobs.  You fight one mob using noisy powers, and the other mobs just stand their ground pounding their fists into their hands.  Even if they can't hear you, they can see you.

That last one I never got - unless they were all optically challenged, how could the group just down the hall not see you beat up their comrades and come help them. Or maybe they did and just don't care?

[Inc42]

That last one I never got - unless they were all optically challenged, how could the group just down the hall not see you beat up their comrades and come help them. Or maybe they did and just don't care?

"Nah, Frank's got those 8 super powered guys. Right Frank? ...Frank?"

The NPCs in City Hall that walked on invisible floors several feet above the actual floor.

Enhancements. Story-wise there is no good way to explain going to a store and saying "My Fireball makes me too tired when I use it, do you have anything to make it a bit easier to use? Wait, you only sell TECHNOLOGY ways to make it cost less. Dang. I need a SCIENTIFIC way to do it."

[Eoraptor]

"Nah, Frank's got those 8 super powered guys. Right Frank? ...Frank?"

The NPCs in City Hall that walked on invisible floors several feet above the actual floor.

Enhancements. Story-wise there is no good way to explain going to a store and saying "My Fireball makes me too tired when I use it, do you have anything to make it a bit easier to use? Wait, you only sell TECHNOLOGY ways to make it cost less. Dang. I need a SCIENTIFIC way to do it."

this sounds too much like a viagra ad... "you know sixty percent of superheroes over level 23 have problems making and sustaining fireballs"

[Felderburg]

Enhancements. Story-wise there is no good way to explain going to a store and saying "My Fireball makes me too tired when I use it, do you have anything to make it a bit easier to use? Wait, you only sell TECHNOLOGY ways to make it cost less. Dang. I need a SCIENTIFIC way to do it."

I always wondered about things like heart implants and cybernetics, from a conceptual point of view. So you just swap those things in and out like it's nothing?

[Blackout]

I always wondered about things like heart implants and cybernetics, from a conceptual point of view. So you just swap those things in and out like it's nothing?

Speaking of which it doesn't just apply to science and tech stuff either, even natural gets affected
"Ok I'll learn the ancient incredibly complicated martial technique of DRAGON!....for only one attack....instantaneously...and am capable of immediately forgetting it if I wish...also even for ranged attacks"

[Inc42]

I think one of the magic SO's or DO's was a magical ring that increased accuracy, I wonder how many of those rings my fire/fire blaster was squeezing on his fingers back in the day?

[Blackout]

I think one of the magic SO's or DO's was a magical ring that increased accuracy, I wonder how many of those rings my fire/fire blaster was squeezing on his fingers back in the day?

Blaster be pimpin' yo' he the Mandarin ain't got anything on him 

[Super Firebug]

The fact that the moon rises in the south. I never got over that one. (I was a science fan in school, especially astronomy, which I still love. So, yeah, I noticed.)

The fact that you could use anything - fire, rockets, tornado - inside a building, and do no damage to it whatsoever.

[Floride]

If I open up a lament box, pour in some spiritual essence and an alien blood sample, stir it with an inanimate carbon rod and recite some source code, I'll increase my healing ability!
Because I'm a hero, and this is.... what we do??

Regenerative Tissue: Regeneration

[Inc42]

The architecture inside the office buildings clearly being designed by a mad man. How practical is it to go up an elevator, walk through long winding halls, up some stairs, down some stairs, and finally get to the next elevator? And HOPE that is the one that you need?

And where were all the offices anyway? We might see a couple cubicles and conference rooms, but not nearly enough to warrant all those hallways.

[Super Firebug]

The architecture inside the office buildings clearly being designed by a mad man. How practical is it to go up an elevator, walk through long winding halls, up some stairs, down some stairs, and finally get to the next elevator? And HOPE that is the one that you need?

And where were all the offices anyway? We might see a couple cubicles and conference rooms, but not nearly enough to warrant all those hallways.

Yeah, the hallways seemed designed by a Dungeons & Dragons mapmaker. And what about all the wasted, unaccessible space on each floor, assuming a standard, four-sided structure?