Ah, OP, it was a thoughtless comment but he apologised. Also, if he puts himself down too in front of you, he likely doesn't see criticism as damning as you do anyway. Most importantly he apologised the minute he realised it upset you, and this is not a regular habit. In fact he's normally quite complimentary as you've said. Unless he's stopped having sex with you or being affectionate, your arms clearly don't bother him. It was just an observation, though an insensitive one.
Be careful of expecting perfect behaviour at every point from a partner. Because unless you have never in your life made a thoughtless or insensitive comment to anyone ever, you owe a loved one the benefit of the doubt that it wasn't malicious. If he had defended his position or not apologised or did it regularly, that's a red flag. None of those apply here.
Also, we need to accept that as much as our partners love us, they don't have to love every single thing about us. Of course, it's better if they never tell us, but if you spend years and years with someone, an occasional slip up could happen. What's important is you immediate let them know it hurt you and let them apologise.
My bf once told me he loved how soft my arms were, and loved squeezing them. Im a size 6 but think my arms are flabby and so felt conscious about the comment: he immediately apologised and hadn't realised my arms were a sensitive topic as I'm so slim and had never expressed body insecurities. No drama, we moved on, he hasn't said anything negative since and life carries on. However, I then decided to work on my arms as they'd been bothering me long before I even met him, and I knew I needed to do more strength training anyway. So if you are self conscious about your arms, you can tone up but do it FOR YOURSELF only.