Dotted line in a pdf changes spacing when exported InDesign

Open one of the "bad" PDFs in Illustrator and see if the path for the dotted line has been broken up into separate segments.

What are your Export Settings?

I have a pdf with a dashed line in my document, 

Is this an InDesign document into which you've placed a PDF with a dotted line? If so, I'd echo Willi's question "What kind of PDF is it?" and I would add "What app was used to produce the PDF?" You can find the name of the app used to create the PDF in File -> Properties in Acrobat. 

Secondly - you made that dashed line with the Line tool and the Stroke panel, right?

(I only ask because once I encountered a clever but inexperienced InDesign user who, when they needed to make a dotted line, would draw the line, then use the Type On Path tool, and fill the path with bullets separated by spaces. They'd tweak the appearance of the bullets with the Fonts panel and the spaces with tracking. Then, when the font failed to embed, the final PDF would look kind of like your second screenshot.)

In addition to the qustions that @leo.r asked, does it als print incorrectly?

 

By @Projekt35644674mrbx

I wonder if this can be affected by the Enhance Thin Lines option in Preferences > Page Display?

Do you see the irregulatority see, when you zoom in?