I'd try standard troubleshooting methods in InDesign:
(1) There could be corruption in the InDesign document. Save as an IDML document (File > Save As > InDesign CS4 or later). Reopen and try again. Saving as IDML can remove corruption, then try creating the PDF again.
(2) Restore you InDesign preferences:
Then try creating the PDF again.
A screen shot of the master page wouldn't hurt, with frame edges showing.
How are your master pages set up? Do you use a black bar on every seperate left and right page or do you use one black bar on the keft page that you extend to the right page? Use two seperate bars on each page and test again.
Not sure what happened to be honest. But the problem seems to have resolved itself so I am all good now. Thank you everyone who tried to help
What I think is that the black field is overlapping the spine. You should always split items from the master at the spine.
Even if you have split it, it could happen due to rounding errors. E.g. a A4 has the width of 210mm, but InDesign calculates internally with dtp-pt, 1pr=1/72inch. So it could happen that the rounding causes that the item from the right page of a master spread begins at the left. That is why I let start these items at 210,001mm, slightly moved to the right, invisible for the human eye, but it works to solve such a problem.