The short answer is yes.
The longer answer is that it's not a "conflict" per se, but it will cause you to end up in the wrong state at the wrong time. The value of each variable is stored in the game, and used to describe the current state of events. As an example, in vanilla FR, var 4055 is used to describe the state of many events involving Prof. Oak. When it's set to 0x0 (0000 in A-Map), that means you haven't met the professor yet. It's set to 0x1 while he's escorting you to the lab, then 0x2 while you're choosing a starter. There are script tiles with var number 4055 and value 0002 that prevent you from leaving without choosing a starter, and they're disabled when you choose one because the script for choosing a starter sets var 4055 to 0x3. That then activates the script tiles for the rival battle in Oak's lab (var number 4055, var value 0003), and so on and so forth. You should keep a document listing all the vars and values you're using and what state each combination means.
So if you use the same "0x4060 0x1" twice, it's not like the game will crash or anything, but when you get to the second event, var 4060 will already have a value of 0x1, meaning you will need to change the value in A-Map if you want to recognize it.
