I believe this is not a bug, the LMB to activate nitro is GTA SA related and the LMB for lights is script related, hence they can overlap and cross.
What you can do however is change the ''key'' to activate your Nitro, this can be done by changing the assigned key under ''Fire'' at Vehicle settings. Clear out the LMB and assign a different key (one that is not assigned to a different task). [The highlighted part is where you change stuff]
Another solution so that you won't have to change anything at all is just literally double clicking LMB, the first click is to activate nitro and the second is to bring the lights back on/off.
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