I'm assuming you found it in the burner tube and not the propane line coming into the water heater. Several possibilities? -- rain forced in by high winds, water from washing the unit blown in from hose pressure washer, condensation from the propane burning(propane does give off quite a bit of water vapor when burned)
Has your unit been in storage or have you been using it this winter down South? Any of the above could happen in either situation but unlikely if unit is/was in storage and furnace not running while in storage.
I'm sure there will be other ideas come along here shortly!
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