Cutting tools exert wedging forces, which can lead to damage on materials or parts. Hence, we use sharp and narrow tools such as skalpels, one option in this case.
Parts on a sprue means that on one side of the cut there is a 'good' side that needs to be protected, while the other side of the cut would be 'waste', i.e. the sprue. Hence, one can or should use a tool that has an assymetric cutting edge, so that the wedging forces only act on the waste side.
There seem to be various cutting pliers with such a configuration on the market.
Personally, I am using so-called 'cutting tweezers' as used by watchmakers to shorten watch springs:
Random picture from the Internet for illustration onlyThe assymetric cutting head allows one to access also tight spaces, say between neigbouring parts on a sprue. They are not cheap, but when treating them carefully, should last a life-time.
These tweezers are also good for nipping something off flush on a surface.