There is indeed a limit on the number of fields. Instead of having many different fields maybe you can create a common schema across all your documents - or index these documents in to different indices instead, where you can have of course differently named fields (again up to 1k).
You may want to take a look at the elastic common schema for some inspiration.
See more at https://www.elastic.co/blog/brewing-in-beats-introduce-elastic-common-schema
--Alex