I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue:
we encountered an issue with our Cosmos DB for Mongo DB 4.3. When we execute the same request (using mongoose 5.13), it fails randomly (error code 50 ExceededTimeLimit). The confusing part is that the db table is still empty. We took a look at the mongodb status page, but there was now error displayed. Also, the same system configuration worked last week. After some trial and error how to solve the issue, we recreated the table and added a single dummy data. That seems to have worked, but we're still not sure if that was really the problem.
So we wanted to ask if there is someone with a similar experience or an idea why an empty table could lead to an ExceededTimeLimit error?
Solution:
as mentioned, we recreated the table and added a single dummy data. Since then we got almost no errors. I'm not sure if the recreation of the table or the adding some data fixed the issue (which would be still strange enough). It's just odd that other database with greater workload and data stored (having the same RU limit) ran smoother during the same period.
If you have any other questions or are still running into more issues, please let me know. Thank you again for your time and patience throughout this issue.
Please remember to "Accept Answer" if any answer/reply helped, so that others in the community facing similar issues can easily find the solution.