How to force a running migration to stop
Did you try migrate-reset-status, and possibly with --force:
https://www.drupal.org/node/1561820

Otherwise I typically restart PHP manually once (restart your webserver) and then use Drush to rollback all the migrations to try again fresh.

EDIT

I rarely use the UI as everything is usable and scriptable via drush when using Migrate. And trying to use a webserver to check the status of long-running tasks can be error-prone.