Automatic filtering is annoying, but there are plenty of tools that will scan your resume and tell you what keywords they find. I once spent weeks crafting a catchy looking resume with a fixed width font and ascii art. It didn't get any responses, and I didn't understand why until I put it through one of these scanners and realized that the program I had used to save the PDF had strangely encoded all of the text in reverse, so I wasn't passing any of the automatic filters. The takeaway: test your resume with a scanner!
It sounds like you could have just opened the PDF that was generated to double-check it too. Sending off a derivative file without proofing seems like a big YOLO move to me
A lot of these scanners went down a few months ago when one of the API services (not sure which) stopped working, but if you have a newer link please do send!