Placing a tracker "sets" your relationship with the futas to 0. But that happens imediatelly after the prologue, when you'd at most have like 2-3 relationship points with Anita and Samantha if you went along with their prologue activities. A.K.A the downside is basically nothing.As of now not really I play with trackers on and have gotten all the scenes in the game haven't seen any downsides to it as of yet.
Placing a tracker on the GF on the other hand sets your starting relationship to 50. It is easy to grind out her relationship back to 100 since hanging out with her in your room is a guaranteed activity, but, specially if you are playing on hard, this might lead into her cheating on the player very early in the game.
Overall trackers are worth it anyway just for the convenience, the downsides are negligible.