After being over-exuberant with Paste-Aligned, I have found out the hard way that duplicate Pipes in the same place do not show in Warnings. Pipe Fittings do, but not Pipes.

The best way I found to get rid of duplicate pipes is click on each pipe and see if it turns red or stays grey. If it stays grey, I can hit delete.

I also do a crossing selection and look at the number of elements selected in the right side of the Status Bar to see if there is a problem.

It is all quite a bit of work, so next time I will be more careful as to avoid the problem in the first place.

This is the entire error report after duplicating two Pipes and One Pipe Fitting:

Error message
Elements There are identical instances in the same place. This will result in double counting in schedules.

Elements
Pipe Fittings : Pipe Elbow : Standard - Mark 2 : id 452297
Pipe Fittings : Pipe Elbow : Standard - Mark 3 : id 452318