I've seen inconsistent behavior before, between Compile Sheet and Compile Project.
My example is, if you have component names interfering, normally on compile it generates an error and highlights the offending components; but after renaming them and doing a sheet compile, the highlights don't go away.
That might be sensible because it's only the one sheet, but you'd think maybe there's project information floating around for that sheet compile to figure out.
Go figure, the best way is to do it every way possible (in these cases, compile sheet, project and ERC), and see what the worst conclusions are, out of all of them.
Personally, I hate inconsistency worse than simply ill-designed procedures. The latter you simply add more steps to run around the bug. The former, each step that's okay ceases to remind you of possible problems lurking beneath, and you can forget to complete the full sequence of steps, very easily.
Tim