I am having this exact same problem. Interestingly, if I change the date on my computer’s clock back to 2019 and collect a tcpdump, pt-query-digest has no problem parsing that file. But any file collected now with the correct date gives errors like tvlooy posted above. I can’t seem to figure out why a new year might be throwing things off though.
I have attached a 7z archive with two pcaps, one from last year (working), and one from today (not working). Remove the .txt extension.