There are two separate glitches with incendiary ammo, and it is impossible not to use one of them if you ever run incendiary ammo.
The first is the buggy interaction with other fire DOT effects (Warp, Flamer, Incinerate, Inferno Grenades). This is important not because the DOT itself is added together, but because IA uses the other effect's defense multipliers meaning that IA can no affect shields and barriers, and has a higher multiplier to armor usually.
The second is that there is an error in the formula for updating the DOT rate when the target is hit with subsequent incendiary ammo shots. The formula is setup essentially for damage per second, but it gets the total damage of the subsequent shots added in, which can cause the DOT rate to skyrocket, especially with rapid rate of fire weapons. Fixing this glitch makes incendiary PPR and Reegar significantly less powerful, although Reegar will still be overpowered if you have the sense to take some armor piercing or weakening.
The second glitch is impossible to avoid if you ever use incendiary ammo. It is more limited with slow ROF weapons, but there is still abnormal DOT rate if you hit the target more than once in the DOT window.
It is possible that some automatic weapons would have been buffed more if the IA glitch didn't exist.
Some other bug fixes that would alter the game:
Phantom DR applied to clients
Phantom's absurd 75% DR would have probably resulted in either less buffs to her hp, or possibly an alteration in some Cerberus waves at higher difficulty. However, it looks like the idea was that she was only supposed to get DR when dodging / flipping and if that was fixed it may have ended up as a wash.
Enemy Pathing is Inefficient
And many times buggy. That's when you get Atlases or other units standing in inaccessible portions of maps. They used an old method for pathing that isn't particularly efficient. It is possible that the enemy unit cap could have been higher if a different method would have been utilized, which would have increased the options for wave composition.
AI Scaling with Framerate
This is probably a bug and it is possible to fix it with a simple change. Would have allowed people to play at much higher framerates and have the same experience as others without modifying the game files themselves.
AI Outside of Difficulty Handler
This technically isn't a bug, but the way the game appears to be setup, AI settings are separate from the difficulty handler meaning that the as you increase the difficulty the AI is more or less the same. What does change are simply enemy HP, magnitude of enemy attacks, and the player's ability to defend against attacks (shieldgate). It may have made more sense to put at least some of these values in the difficulty handler so that you could make higher difficulties have better enemy AI. It may be that they were concerned this may reduce performance at higher difficulties, I don't know. But to me it would make more sense to scale AI rather than enemy HP. This could result indirectly in better weapon balance in that lower damage weapons don't become automatically less useful at higher difficulties.
Shockwave Geometry
Shockwave has issues with the way it was designed and what sort of variables are modified. If it was done differently then the Radius evolution would have been much more valuable and we would have had a power that is fun more consistently. Probably would not have received detonation evo buffs.
Snap Freeze
Power is bugged to hell. Reach causing CE damage to double, Tech Combo reducing damage of combos. SF priming all targets for CE which if it isn't a bug is a stupid design choice. This power would be much better if these issues were resolved. Nevermind that combos it detonates are centered on the player due to the way that combo detonations are handled.
Penetration Based Multi Hits
Assuming this is a bug, which it likely is. Probably would have resulted in less buffs to some enemy HP. Also semi-related is whether or not AP Ammo consumable is really even supposed to have 0 damage penalty for penetrating cover. The SP power has a 50% damage penalty which makes it substantially different, IMO.
Turian Stability
Doesn't work off host. If it worked properly who knows if Turians would have gotten buffed passives.
Reegar Disappearing Shots
This is somewhat applicable to other weapons. Reegar fires way too many projectiles per second due to the ROF and the 8 pellets per shot. The game cannot resolve them all so many disappear from the space time continuum. This results in differing damage on console than on most PCs. It is more than possible that if Reegar had lower ROF the final damage values would have been different.
Weight Adding Weapon Mods
Probably has to do with the fact that these add weight when applied, and they aren't updated when you reinitialize a character who already has them applied. This indirectly affected weapon balance, but if it worked than some of the mods would have likely been buffed or had the penalties reduced for some mods.
Blade Armor Melee Damage Returned
There is an error in the formula for blade armor melee damage returned in that difficulty multipliers are not handled correctly, so BA does less damage to melee units at higher difficulties. This is pretty minor and would have only meant that BA might not have been buffed as much.
Shield Regen FPS Dependent
This isn't a big deal in stock game configurations, but if you uncap framerate than shield regen can trend to 0 for some characters. It was possible for Drell without maxed fitness to never regen shields at higher framerate. Again, without this sort of thing they could have allowed a higher fps cap without modding the game. Not a big issue if you play at "stock" settings.
There are obviously more bugs.
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