Yes, you discovered a major security issue.
This is why pausing scripts shouldn't be done. An exterior FileMaker file can pass a call into that paused file and halt the running script, corrupting your workflow and potentially exposing data it shouldn't. (Steven Blackwell demonstrated this during his DevCon session last year, and it was scary.)
I wish I had a t-Shirt like this:
On the front: Pause/Resume Script ?
On the back: Just don't do it.