I had similar issues… almost every font I tried had artifacts after I applied Fillet Caps in C4D. Also, artifacts got worse when I checked the Constrain box in Caps options.
After tweaking for hours I found a fix…
SOLUTION: add / subtract anchor points in Illustrator
After you convert your text to outlines in Illustrator, use the Anchor Point Tool to add and/or subtract anchor points.
Erik Topolski
C4D + CS4