When merging tickets, it should not allow you (or at least should warn you, requiring an extra click) if you're attempting to merge tickets from different customers.
I've had situations where I've had multiple Open tickets with the same subject from different customers who coincidentally had the same issue at the same time (or were just really bad at writing useful subject lines and I hadn't got round to changing them to better ones yet) which looked at a glance like the all-too-common "reply creates new ticket". I've only merged tickets wrongly once that I know of but it's very easily done and I feel like it really shouldn't be.