It might be worthwhile going back to your agent and asking for an example of the sort of thing she means. 'Strengthening' isn't much to go on.
It could mean making sure each character speaks with a distinctive voice--for example, I have a character who rambles and rambles and rambles. I actually love writing him. So if I wanted to make his voice stronger, ie more like himself as I perceive him, I'd probably add more rambling...except I think any agent would say "Enough with the rambling Ms Sqrl!". He also uses very tame language, such as 'goodness' and 'dear me'.
However, he's also a mild fellow who doesn't get into arguments and fights, but loves explaining things. So I have other characters comment, for example, on how when he does something like make a slightly rude remark about someone, that for him is the equivalent of getting into a fight with them. This all goes to reinforce the idea that he's not aggressive. Characters should always act in character except when they don't--frex, once this mild-mannered rambling guy gets so excited about something that he actually shakes the narrator. Extraordinary circumstances change his behaviour.
One problem I had with the novel I'm currently revising is that although the reader's told that the protagonist is a very jealous type, there wasn't much evidence of it in his actual behaviour. So I strengthened that aspect of his characterisation by having him behave very jealously on specific occasions. That meant new scenes and different slants on old scenes. If you've defined your character as 'x' you need to show the reader that they are 'x'.
HTH