1. If a 2x2 was scrambled wrong and a 1 move solve was done should it be allowed?
A2. If a 3x3 was scrambled wrong and a 15 move sub4 solve was done should it be allowed?
A3. What if that solve was in the WC final and would cause them to drop from 1st to 4th if DNFed?
A4. If a 3x3 was scrambled wrong and a normal solve by an average cuber was done, should it be allowed?
During a competition, if the misscramble is noticed, none of these should be allowed. It's against regulations, right? The solve should be removed and the competitor should be given a replacement solve, just like if they were given the same scramble twice, or handed a solved cube.
The problem is when, after a competition, someone gets a DNF due to a situation completely out of their control. Then there is no time to give them a replacement solve, so getting rid of the affected solve is a potentially huge penalty (especially given that we only even look at solves that are good enough to be on video, i.e. mostly regional records or official PBs). In case A1, the delegate and/or judges are idiots and should probably be "fired". In the other cases, the competitor performed a legitimate solve of a clearly scrambled cube that they had no prior knowledge of - let it stand, and if you want to punish someone, punish the scrambler.
Aside from those situations which are not the competitor's fault, we have:
B1. Regulation violations that are the competitor's fault, were accidental, and (at least) might have given an advantage
B2. Regulation violations that are the competitor's fault, were accidental, and did not give an advantage
B3. Regulation violations that are the competitors fault, were deliberate, and (at least) might have given an advantage
B4. Regulation violations that are the competitors fault, were deliberate, and did not give an advantage
B1, B2: Who cares? Accidents happen.
B3: Cheating. Disqualify an appropriate number of solves, and suspend competitor for an appropriate amount of time, depending on the actual situation.
B4: Not sure why someone would do this. But if you are sure it gives no advantage, give the competitor an official warning not to do it again, and take further action only if they keep doing it.
Re: exposing parts of the puzzle. Are you guys serious? What's the point of a cover and timed inspection then? What if someone uses a non-Fridrich method and this actually helps them out? And what do you plan to do with people with alternate color schemes (e.g. Mike Hughey scheme which swaps orange<->red and yellow<->blue from the perspective of holding white/green steady)? I guarantee this will cause more problems than it solves.