Updating to 5.3.7 fixed my issue.
I”m experiencing the same issue, WordPress 4.5.2 and ACF Pro 5.3.0, the Custom Fields are displayed on the left side on my custom taxonomy but not when I try to edit a term. I already disabled every other plugin to exclude an issue with one of them and I don’t have any java script errors in my console, only this probably unrelated notification:
load-scripts.php?c=0&load[]=jquery-core,jquery-migrate,utils,underscore,wp-util,wp-a11y,updates&ver…:9 JQMIGRATE: Migrate is installed, version 1.4.0