You are right: on an iPad every light tap on the map added a waypoint, and so did a tap that just missed a button. I will make some improvements soon!
On a tablet you now hold your finger on the map for a moment (a ring fills round it) and the waypoint appears when you lift it. A quick tap no longer adds anything, and a touch right next to the map buttons never adds a waypoint. Mouse and Apple Pencil still work with a single click. It'll be in the beta with the next update (end of the day).