I'm not sure how you'd pervert wish into a literal but undesirable fulfillment of 'more X'.
'more x' for 1 round rather than permanent, 'more x' as a permanent dispellable effect, promptly dispelled.
If the player asks for an instantaneous non inherent bonus, have it be truly instantaneous, IE expired before the player can regret being a munchkin wasted their wish. Another option is belanced buff/debuff, they get +1 and -1.
Another option, crazy nonstandard wishes are based on the idea of infinite power to produce the reward, the wish isn't a standard balanced, listed effect, it's ANYTHING, which is infinite pre-definition. Use that against them. So... the universe was created by the wizard primeval, with a nearly perfectly worded wish, which bans other wishes in certain circumstances (especially ones that provide bonuses) either as a result of a programming error in clause h874-m (how to handle bonus pay for mercenary work), or because the wizard was a refugee from another reality where wishes weren't so capped, and lived in terror of the idea of wishes to destroy the universe/make gods/etc. No, you can't ever know what the wording of the wish primeval is, you can't even comprehend its existence, clause a003-a (how to prevent the destruction of the universe).
tl:dr: If wishes can do anything, you live in a pocket wish-created universe where certain wishes have been preempted by wish.