At equivalence the concentration of HIN molecules equals the concentration of In- ions, so there are therefore an equal number of yellow HIn molecules as there are blue In- ions, so the appearance of the mixture is blue-yellow, ie green.
H+ ions do remain at equivalence - they are not all used up. Because [HIn]=[In-] at equivalence the indicator dissociation constant, KIn equals [H+], which in the case of bromophenol blue is about 1x10-4. This does not represent a neutral solution, nor does it for most other indicators. However, the shape of the pH titration curve shows that this is irrelevant, since pH often changes very dramatically at or near equivalence.
You need to look up the principles involving the use of indicators.