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Can you tell us more about your stencil, or perhaps zip it and attach it to a post? Are you running the most recent version of OmniGraffle on your iPad? Which version of iOS? Does your stencil have images pasted into it?

I haven't had any problems with stencils lately; at one point the app was pretty finicky, but it has been improved quite a bit. You're 100% positive that it tried to open it in OmniGraffle? I ask because when I ran a test just now, emailing an identical stencil saved both as a flat file and as a package file, my iPad thought one of them should be opened with OmniGraffle and the other with OmniOutliner (even though they both had the same .gstencil extension), and it should come as little surprise that OmniOutliner didn't know what to do with the stencil.

If you aren't comfortable posting your stencil here, you could use Help->Send Feedback in the Mac app to send it to Omni with any text turned into strings of x's.