1) Some games are incompatible with some 1541 ROM revisions. Hydrax and Standng STones are prime examples. Them NOT working on your ccs64 installation is NOT an emulation bug. Replacing 1541.rom with the one from your actual 1541, or the one that comes with VICE should solve the issue. Gemstone Warrior and/or gemstone healer are also prime examples here. They are notoriously finicky about drive rom revisions, especially the earlier revisions of the game. I've actually ran into trouble on a real breadbox with Gemstone Warrior.
2) "But this worked on c64s! Your emu is bugged!" A large number of old images on arnold were hacked to work on c64s back in the day, and will NOT run when transfered back to a real c64. Most notably, the version of demon stalker that's on most sites in .d64 format that worked fine in c64s will not run in ccs64. however, a proper .g64 from original works fine. Again, gemstone warrior and gemstone healer are good examples here. Some versions are "C64S-hacked" and this causes trouble. and yet ANOTHER example is web dimension from the c64 15 pack, and top fuel eliminator. I had to unhack web dimension myself, and that top fuel eliminator has a horrid c64s hack in it. ALso there are some horribly hacked tape files with wacked out loaders out there that run fine in c64s, but will never run on a real box. I know because I'm responsible for a few of em. (laugh)
3) kernel ROM bugs. The easiest example of such a bug to come by is pharaoh's curse. this game will bomb upon startup if tried on a revision 1 c64. It also never worked in c64s, for the same reason.
4) "The game doesn't recognize the next disk!" 90% of the time, this is either a bad image, a bad crack, or a disk ID problem (the problem being that the .d64 file format doesn't store the IDs properly). If it works on your real c64, sixpack it, and send the sixpack over with star comander, and extract it to a .g64 under emulation. This will usually solve it. 5% of the time, you've ran ito anothr c64s hack, and the remaining 5% or less it's actually an emulation bug.
5) game will not fast load. I list this for completeness sake. try "load normal" instead.
6) pal/ntsc issues. These crop up more often than you'd expect, and even catch the newer cracking groups like Remember by surprize on occasion. Bruce Lee crashing? Try switching to NTSC. Music playing at half speed? Switch back to pal. music a il too fast? use PAL. music a il slow? use NTSC.