macOS Sierra 10.12.5
Alfred v3.4 
Alfreds clipboard history seems to interfere with LibreOffice. When clipboard history is enabled pasted text to LibreOffice will always be the last thing copied in LibreOffice. When Alfred is not running everything works fine. Disabling Clipboard history also seems to solve this.
I can't reliably reproduce this. It always happens when I work with LibreOffice, but I can't pinpoint the exact event, that triggers this bug.
One interesting observation: This also affects TextExpander snippets. Inserting any snippet will paste the same text that was copied from inside LibreOffice before.