People keep reporting it as a bug now that a modpack has enabled it. Either the option needs to clearly state that it is meant for adventure maps and WILL override beds, or it needs an additional property that only sets the spawnpoint if it's not set to a bed yet.

For now, you can disable "Set Spawnpoint on Activation" in the waystones.cfg manually.

Option removed in 1.14, adventure maps can use observer / command blocks to set the spawnpoint when the player activates a waystone.