I don't know what the comments were, but one thing I'm sure of is that they weren't silly at all. The business of publishing is a serious one, and if an agent bothers to give feedback - which they had no obligation to - then you can be certain that all their comments are serious rather than frivolous. This doesn't make them right, but it does mean they won't be silly.
The trick is to work out where the comments are coming from. Why do they seem "silly" - or irrelevant, misjudged, inaccurate, off-beat, ridiculous? What are the comments telling you about your writing? It's obviously not as clear as you think it is, not when someone has got it so wrong. What are their suggestions indicating you address? If you disagree with those suggestions, then ask yourself why? Work backwards and find out if there is an underlying problem.
I sent my first novel out, and one of the suggestions was to strengthen 3 of the 4 viewpoint characters. My reaction was to take the opposite route - ditch 3 of the 4 viewpoint characters, and concentrate on one viewpoint. That was the right choice for me, but it took a "silly" suggestion to make me realise what the underlying problem really was.
NB Sometimes agent suggestions are silly. One agent said that I was wasting my time with the novel and should give up. Maybe they were right and not so silly, but here I am, still writing...