Unless they're actually a robot, it's inevitable that a therapist will feel counter-transference - probably pretty frequently. The important thing is that they remain aware of it and reflect upon it - so it's probably a good sign that your T is doing that. Having said that, I'm not sure what his aim was in sharing it with you - as others have said I think it's worth asking him more about it - in fact I'd always recommend questioning him if he says anything you're confused or unsure about.

On a side-note, Moment and Wrk, your discussion above about the T bringing up counter-transference being a positive thing is really interesting and feels so relevant to me - last night for probably the first time, my T (although he didn't actually use the word counter-transference) said that he was going to reflect on something and I felt so pleased about it. It showed me that he's really thinking about our relationship and the feelings and thoughts I bring up in him. I shall probably write some more about that in my thread on this forum.