Traditionally, English speakers are taught not to split infinitives, that is, not to put anything between to and its verb. That may be what your friend is objecting too. But the ban on split infinitives is (rightly, in my opinion) derided by a large number of linguists and grammarians.
To my mind, the more substantive issue is with the use of not only. For perfect parallelism, the construction should be either of the following:
I found Bob not ADJ but ADJ.
I found Bob to not only VERB but VERB.
You’ve mixed the two: I found Bob to not only VERB but ADJ. So, if you fill in the ellipsis here (which is everything up to not only), you end up with:
I found Bob to not only VERB but [I found Bob to] ADJ.
Needless to say, I found Bob to ADJ is ungrammatical, which means that the large structure is also ungrammatical.
One solution is, for once, to follow the proscription against infinitive splitting:
I found Bob not only to have a good sense of humour, but able to dodge flying arrows.
But I’m not crazy about the mixed construction. I think a better option is to turn the adjectival phrase able to into a verbal phrase, to be able to, so that you have two verb phrases:
I found Bob not only to have a good sense of humour, but to be able to dodge flying arrows.