in the game Clystron, there's a visual bug, which CCS64 doesn't seem to emulate. It's a few stray pixels visible every couple of frames when you go to the right. I have verified that this glitch appears on a real C64. Below is the screenshot I took from Hoxs64, which shows the missing flaw.
I am having difficulty seeing a glitch with this screen-shot - what is the graphical glitch? I use C64 Kernel Revision 3 with CCS64 (CCS64 gets released with C64 Kernel Revision 2) and it looks the same as Hoxs64 does to me (thereagain I've only looked quickly). So, perhaps try that. Which crack are you using? I downloaded mine from:
http://c64.hardwired.hu/