If you create a pipe in one go from connection to connection, you have a single pipe segment that can be deleted, upgraded, paused, etc. with one click.
But if you piece it together, you will have seams that divide the pipe into multiple segments.
This is not only annoying when you want to upgrade or delete, it also means you are forced to have a pillar there that you can't move or get rid of.
The only two ways to join the segments right now is to re-crate the whole pipe, or, as a workaround, create a pipe connector there, connect a dummy segment to one of the sides and then delete the stub. This will also delete the pipe connector and join the segments.
Either always auto-join pipe segments or add some command to explicitly join the segments (prefer the latter).
Edit: Oh, I forgot. The same problem also exists with belts!