EMS SQL manager permission problem
The best thing you can do to understand this behaviour better is to ask the software vendor. If you don't want to grant those permissions, lodging a bug report might be appropriate.

I'm going to hazard a guess that EMS SQL Manager is trying to be too clever, and check whether you have Alter_routine_priv or Create_routine_priv so that it can return a warning or error before it tries sending your ALTER ROUTINE to the database. 

Most SQL Editors run lots of queries in the background to support "IntelliSense", speed up common queries, or provide background information, and a lot of the time they just don't make any sense (some of them are downright frightening).