Liz from YouTube support posted a thread at the YouTube Help forum confirming a wide spread bug with commenting on YouTube videos.
Liz explained the bug as follows:
We've seen many of you report that you're having trouble with comments: more specifically that you receive notification of a new comment on one of your uploaded videos, but the comment never appears. This is an issue our team's aware of and is currently working on a fix. Comments should be working as intended again this week.
Google said they fixed the issue with the comments on YouTube, but some seem to still be having issues.
Forum discussion at YouTube Help.