Not clear what you mean. Are you trying to insert a pdf into a container field?
Are you uploading via a script? What does that script look like.
if the upload dialog is presented via a script, I wonder if it is using a plugin that you may have installed for 15 but not for 16?
I bring up the script because there is a slight change in behaviour with the "Go to object" script step in v16
FileMaker 16.0.1 data integrity disclaimer | FileMaker If you are using that script step and go to object is failing then the script will behave differently.
E.g. if you are using go to object to go to a specific portal before uploading the file.