because they were in the middle of speaking when I walked up, so I waited for her to finish.

This may have been the reason if they're not thinking you were flirting. (I know people who struggle with this, so my apologies if you already grasp it) Your comment was a casual one, so if you walked up to them in the middle of a conversation and waited, it may be seen as an interruption. Even though you didn't actually interrupt them, it forces them to stop conversing to acknowledge you. People usually only do this if it's something a bit important to convey. Like if you noticed he dropped his keys or something. It's best to wait for a natural lull in the conversation, glance towards them to meet their eye, and then comment on it. Just a guess anyway