Random Vectors/images color inverted in print, but not in PDF. Where does the fault lie?

Sent a PDF to the newspaper printer and some of the images had inverted/strange colors. However...
In one case I had duplicate images of a pink vector flower. SOME of the flowers were inverted, to a dark blue/black, and some were fine(pink). These were embedded vectors.
In other instances vectors, went from orange to blue/black, pink to blue/black, and yellow/white to blue black. I specify because in one vector image, a ring, the ring was yellow, but the diamond was white, and it all changed to the same blue/black in print.
Finally, there were two greyscale Tiff photographs of a pair of ladies. These are not embedded, and have not been altered at all and since the last time this paper has been printed, (which printed fine). This time, they were inverted. Nothing else on the page was inverted.
As far as I can tell, there is not a separation issue, and I have saved the file from InDesign CC to pdf using the same settings as dozens of times before. The pdf on my end looks fine. The printer says they just print what they receive, but as far as I can tell, there is no issue on our end. The fact that some duplicated images printed fine, and others did not seem to confirm this. Everything is properly linked. Has anyone else experienced this problem? Is this a pdf, InDesign, or even an adobe problem at all, or it is something on their end? I have heard of inverted colors before, but can't find a solution (especially as I can't even see the problem on my end.)
Using Windows 8, up-to-date InDesign CC, and Acrobat Pro, Illustrator CS6 ver.16.2.0 64bit
I have no idea what the printer uses.

Where does the fault lie? - in an environment where they (the newsprinter) collect up front, have no responsibility for quality and arrogantly believe, perhaps correctly, that you'll be back with another paying job in the future.
Check the file you sent via Acrobat Preflight or Output Preview for RGB elements.
Check the file you sent via Acrobat Preflight - Checks - For Transparency Used
Do any of these elements off color involve rgb or interact (with or near) any transparency?
(InDesign could show these attributes via the links panel or a Live Preflight. Both can be (probably should be in your case) changed via the PDF Export)

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