Thank you for your reply.
I don't think that is a problem of the functional (I tried also other xcf like tpssh and pbe0).
With aug-cc-pVDZ I have no problems, as well as with bs (external or built in) without diffuse functions (6-31G*, 3-21G*, cc-pVDZ,...).
The problem is that B3LYP/6-31+G* level is not working for some of my systems (namely 12 out of 48), so it is not a systematic error. My guess it's that for these systems linear dependencies are more crucial....thus, I'd like to remove some of them (if it is possible).
Thank you once again
Best regards