Knowing which mods you are running is essential, because it could tell us if there are incompatibilities which cause CTD. Although buggy, the stock game + the v.1.5 expansion (U-boat expansion) will not crash or show glitches like you mention - that is: if installed correctly.
When installing, you should install to something like C:\Games\... and not in the Program folder, then make sure all games files are not write-protected.
Only limiting your mods to popular megamods and not adding more without knowing what you do exactly should run the game fine. Mods like Ralles Modpack, TMO+OTF, RFB, or FOTRSU. If you make a bad mod mix, then the problems you mention will certainly arise.
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