Commas are valid separators for BED12

[arq5x]

Columns 9, 11, and 12 can and typically do have commas.
https://bedtools.readthedocs.io/en/latest/content/general-usage.html

[brwnj]

a comma is not a valid field separator ([ \t]+) and is only allowed to be used within a field, so unsure what you're trying to point out.

having the commas can throw off the auto-detection of the actual delimiter so I may have to double check fields 1-3 for whitespace when comma is found.

[arq5x]

Got it, yes commas would be disallowed in columns 1-3,6,10