I've been having the same problem since upgrading to Oxygen. I haven't been able to reliably reproduce the issue.
The workaround suggested by @howlger has helped and is less intrusive than blowing away the entire workspace:
.metadata\.plugins\org.eclipse.e4.workbench\workbench.xmi
file or just rename it so you can bring it back in case you need to revert.This is a pain, but does remove the duplicate elements from toolbars.
I also found that customizing the perspective doesn't work for duplicated items, but does for non-duplicated:
had this issue also on eclipse oxygen. Thank you for the hint, worked like a charm
This is the only thing that has worked for me...at one point of time these duplicate icons were occupying half my screen and this worked perfectly.