I'm not sure what tools and applications you have at hand, but I opened your SVG in Adobe Illustrator and saved it as a PDF. The result did not have the glitches you showed.
Are you able to take a similar route and incorporate the results into your thesis?
I do get a similar glitch using the SVG in Word and PDF Maker, but converting the SVG to PNG in illustrator results shown below on the right. If you're willing to convert the file format, the result seems to do the trick.
I'm not able to incorporate the pdf into my thesis because I need to add captions and comment to it, so I need to insert it in the .docx file.
If I convert the document directly with the export option in word there are no artifacts, the problem is that some other vector images I inserted have the problem that the lines are much more thick than what I used in Illustrator.
Would you be willing to export the images out of Illustrator in a different format other than svg? The sample I showed (right image above) was opened in Illustrator and saved as a png file. It was then inserted into Word and converted to PDF using the PDF Maker.