As Linux does not support more than 32000 sub-folders, 31998 when you take into account "." and ".." the builds folder can become "full". We worked around this by employing a more aggressive cleanup strategy, but we will eventually run out of folders again.
Can I suggest that builds are not stored in a single folder but instead are stored in a hierarchy where the top level folder is the first 2 digits of the build number e.g. build 12345 would be stored in folder 12/12345.