Barbara Pavlik

If you see this happening in other tools and keeping in mind the provider of MT is deepL - then I doubt we can do much. 
You are welcome to share your source file and confirm your language codes so I can test and clarify behaviour on my end.

Lyds 

Hmm, well the work I do is confidential, so I can't share my source files.  And at the risk of sounding ignorant, what are language codes?

Barbara Pavlik, language codes meaning what would your source / target languages have been set to. Information that along with a sample file would have helped me reproduce the issue. But I understand you are concerned about confidentiality.

In the absence of a sample file:

Try disable any TM you may have in your project alongside MT so its strictly MT that is being used for pre-translation. 
What if you take the sentences it is not translating only, create a new document with these sentences and then try your pre-translate, does it work then?
Do you you feel the issue could be related to file size - have you tried processing DeepL/MT using a smaller file?
I assume you running batch tasks pre-translate at which point you find the missing translations, what about if you do live lookup in the active Translation Memory Window?

Looking forward to ruling out what we can based on your test findings

Lyds 

Barbara Pavlik, language codes meaning what would your source / target languages have been set to. Information that along with a sample file would have helped me reproduce the issue. But I understand you are concerned about confidentiality.

In the absence of a sample file:

Try disable any TM you may have in your project alongside MT so its strictly MT that is being used for pre-translation. 
What if you take the sentences it is not translating only, create a new document with these sentences and then try your pre-translate, does it work then?
Do you you feel the issue could be related to file size - have you tried processing DeepL/MT using a smaller file?
I assume you running batch tasks pre-translate at which point you find the missing translations, what about if you do live lookup in the active Translation Memory Window?

Looking forward to ruling out what we can based on your test findings

Lyds 

Hi Lyds, 

Sorry for the late reply.  The language pair in this case was DE>EN (German to English).  This happens regardless of whether there is a TM enabled.  I made up a test file using a very short document (only 16 segments) that I had previously translated in MemoQ. I just let the MT plugin populate all the segments.  It left three of them untranslated.  Since this doc has already been published online, I could send you the file. How would I do that?

Barbara Pavlik Thank you for your reply and for your added notes. I will send you a private message with a secure link to which you can upload your example document.

Hi Lyds, I uploaded the file last week.  Have you had a chance to look at it yet?

Hi Barbara Pavlik

Yes I did thank you. If you see below, I took your file and was able to perform a full Batch Translate with all segments localised.

I am aware of some cases where segments don't full get localized but that is totally unrelated to DeepL. As you confirmed, if you have seen this happen in other CAT Tools then I suspect there is little we can do. If however you find we can support you in other ways, please do let us know.

Lyds