Yes I found this awkward as well.

Thanks for your feedback. Would the solution to this be to click the waypoint and have an option to delete?

It would be helpful, still instead of having 2 action buttons that do the exact same maybe it would be better to use one for the second most probable action if it exists (in this case delete), that is if they are not reserving it for something in the future.

2 duplicated here:

Ability to delete waypoints? (geometa.co.uk)

Can't delete waypoints (geometa.co.uk)