InnoDB errors and crashes with MyISAM database?
I have some annoying news for you. MySQL 5.7 has InnoDB enabled permanently. It's in the Docs:


  Important
  
  InnoDB cannot be disabled. The --skip-innodb option is deprecated and has no effect, and its use results in a warning. It will be removed in a future MySQL release. This also applies to its synonyms (--innodb=OFF, --disable-innodb, and so forth).


The number of InnoDB tables have increase from version to version.

I mentioned this Apr 04, 2018 in my old post Restoring XtraBackup from MySQL 5.6 to MySQL 5.7


  MySQL SCHEMA FILES
  
  The number of InnoDB tables in the MySQL schema also changes between major releases.
  
  Back on Dec 09, 2017, I answered ERROR 1031 (HY000): Table storage engine for &#39;proc&#39; doesn&#39;t have this option and discussed when InnoDB tables starting being used in the MySQL schema.
  
  In MySQL 5.6, it was 5 tables. In MySQL 5.7, it went to 19. In MySQL 8.0, all 31 tables are InnoDB


From my old post, I stated that MySQL 5.7 has 19 InnoDB Tables in the mysql schema.

In order to hunt down your InnoDB properly, run this

SELECT table_schema,table_name
FROM information_schema.tables
WHERE engine='InnoDB';


The 19 tables from the mysql schema should appear. If you have additional InnoDB tables, you will have to get rid of or rebuild those tables. If the 19 tables do not show up from this query, you must fix this.

I just noticed you said in your question : Since it moved to mysql 5.7.27 there are InnoDB related errors and even crashes

If you did not upgrade the system tables correctly, mysqld is probably looking for the mysql schema tables to be InnoDB.

Please read MySQL 5.7 Docs on mysql_upgrade and look at --upgrade-system-tables. It should convert the mysql schema tables from MyISAM to InnoDB.

Please do this in a test environment first beforehand.

UPDATE 2019-09-20 18:09 EDT

After a nice chat session, it turns out that there is a lot of temp tables being generated. All the temp tables were using InnoDB, consuming 482MB of the InnoDB Buffer pool. The InnoDB buffer Pool was at default (128M). Increase above 512M solved it.

I also recommended switching every to InnoDB.