Something is odd there.
Normal reasons for /3 wire on a receptacle run:
- Half-switched outlets (tabs broken, 0V between black&red, or perhaps phantom voltage between the switched conductor and neutral or unswitched if the switch is off)
- MWBC (tabs broken, 240V between black & red.)
In either case, black & red would NOT normally connect to the same terminal. Since the breaker didn't immediately trip (sign of an MWBC without the tabs broken, or with black & red connected any other way), look for a switch that will seem to "do nothing" because the switched and unswitched hots are currently joined together.
If red is always-hot, and no switched outlet function is desired, simply remove black from each outlet, isolate it, and leave them wired as they are otherwise. You can join themthe blacks to each other (but not the receptacle) in the intermediate boxes or isolate each one in each box as you prefer. While it's more common for red to be the switched hot, that's evidently not the case here, and that is not required by code.