Get the ID of the custom field affected(eg. Product Manager) with the following SQL query:

select * from customfield where cfname = 'Product Manager';

In this case, the custom field id was 11323, you need replace the number with ID of your custom field. In this query, take note of the ID for fieldconfigscheme.

select * from fieldconfigscheme where fieldid like '%11323';

Run the following query to check if the fieldconfigscheme that attach with issue type and you will find there's different value under fieldconfiguration column and that column value should be identical.

select * from fieldconfigschemeissuetype where fieldconfigscheme = '11351'

Run a query to ensure the 3 configuration exist in JIRA database:

select * from fieldconfigscheme where fieldid like '%11323';

In this case(you may get different result), delete the 2entries from fieldconfiguration table and fieldconfigschemeissuetype. After that, update the remaining one of the entries from fieldconfigschemeissuetype table to null(eg. Any Issue Type in the context)

delete from fieldconfiguration where id in (11351,11391)
delete from fieldconfigschemeissuetype where id in (12348,12349)
update fieldconfigschemeissuetype set issuetype = null where id = 12347