If that is the case Lawful_G then I understand why he is having so many issues. I never reverse engineer skill points as most of the time it is wrong. Instead let HL calculate the correct number based on the Hit Dice. So lets use your 3HD creature with 7 skill points and assume it is an
Aberration which gets 4 Skill Points per level. So at 3HD it should have a total of 12 skill points.
Using your example this means that only 7 skill points where used leaving another 5 skill points listed as unused on the Skill tab. This would be exactly like I mentioned above that those 5 should be left in Red for the next DM. They can decide to leave them unused or like myself I would allocate them quickly to skills I think make sense.
Mostly likely Acrobatics so it can tumble around the PCs.
The main points being don't reverse engineer skills or feats and instead let HL calculate the correct number. If you need a weapon to have a different Crit Range then use a script or tags to change that instead of giving it a feat that is not listed in the stat block.
Hope that helps....