Do you mean an iPhone application or an iOS application that does not include an iPad? Apple will not abandon the application if it is released on iPod Touch, as well as the iPhone (and I saw examples where functionality does not even work on iPod Touch, but it was allowed in any case).
I suspect that you created the iPad app at some point and then uninstalled it but did not uninstall it correctly? Then it will create an iPad version that will not do anything at startup, and this may be the reason for the rejection.
What exactly Apple sent you to its e-mail address, they are usually very good with a reason for rejection.
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