Broken workflows cause this, for instance there is an action going from a state where the resolution should be set, to one where it should not, without clearing the resolution. My plugin highlights these problems in the workflow diagram: https://studio.plugins.atlassian.com/wiki/display/JVIZ/JIRA+Workflow+Visualization+Plugin
Also CSV imports can cause this.
The script runner has a built-in script which can bulk change the resolution on issues, after you fix the workflow, if that was the cause: https://studio.plugins.atlassian.com/wiki/display/GRV/Built-In+Scripts#Built-InScripts-BulkFixResolutions
This might also be worth a read: http://blogs.onresolve.com/?p=84
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