That's probably a valid reason, but don't let that lull you into passing up the condom on the fourth or fifth attempt. I knew a woman who ran out of condoms after four, and got pregnant on five. As I read your post you used condoms each time, and you were not in the fertile window. You should be fine!
So, one thing to always remember is that apps are just guesses and not scientific. :>) They aren't checking your hormones but instead, guessing on the input you've put in when you might ovulate or get your next period. It can always be an off month. And pulling out will NOT prevent pregnancy. The penis emits small amounts of sperm and that is enough to do the job. BUT, I see you say he had a condom on. So, if a condom breaks, it's usually a huge catastrophic tear you see. It sounds like he just had a very small amount of sperm (and probably a pretty weak orgasm).
I'd say you are probably safe with all the info you've provided here. good luck