I don't know if this is a common setup but it looks definitely not usual to me !
That is a lot of users for such a setup!! I assume it is one docker container by user ?
In my company, we began by a Rstudio server open source in a docker container for a small team (5) and when it was proven to be useful for other we switched rapidly to 1 Rstudio pro server then 2 servers, that allowed us to offer better services to the 50 and more users. Just to let you know that it cost sure, but it could ease the administration and be better for users. 
On you issue, unfortunately, I am not sure I can help more. I don't believe it is an issue with the product, maybe more with the setup and the number of user. I think You'll have to wait to see if someone else have done the same and have experience or from someone of Rstudio that may have experience too.
Thanks for the precision by the way! 