If the project has a default Security level, but the field is hidden in the field configuration and it is not present on the screen, then when creating a task via mail, it is assigned this default Security level. So it should be, or is it still a bug? If in such conditions they create a task manually, then the Security level will not be assigned.
The security level is needed only for one type of issue and to be set by default, but in these projects issue are also created via mail with other types of issue and for some reason they are also assigned an Security level.
That's correct, you've set a default for new issues.
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