Usually such problems could occur after a previews code change which has imposed one of the following things:
1. You have a long running queries that are executed relatively often
2. The schema migration is not the first operation with the DB when your app starts any more.
3. You have switched from short living to long living contexts and thus the scope is left open for longer time.
I would suggest you to check if the schema migration is the first thing which happens in your app when it starts, if it is not - prevent any other previous DB operations.
Also you could retry the schema migration in case of this exception several times to find a moment when there is no currently executing query. You can sleep random time interval between the retries. In case you exceed the allowed retries you could give up or use the ForceExecuteDDL method which will execute the script regardless if there are running queries or not but you should know that this could cause errors in such running queries.
As a bottom line I would say that your application logic should ensure that when you perform the schema migration not other DB operations are running.
I hope this helps.
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