There shouldn't be any issues reading PC-burned CDs, but there are some caveats
1. Some older CD drives tend to have trouble with CD-Rs. The best way to work around this is to burn at as low a speed as possible. Specific media type might also be a factor, but I've found that low burn speed usually works.
2. The CDFS shipped in 3.1 is not that good. Filenames aren't always the correct case, sometimes there are MS-DOS filename issues (8.3 and the ol' ~1) depending on how a disc was burned. Probably best to install a different CDFS. AmiCDFS is on Aminet and a good non-commercial choice. Using a different CDFS usually consists of putting the filesystem in L: and using the CD0 file provided with the package.