It is FAR more likely on yahoo's end:
- Yahoo, for whatever reason, seems to have more issues with mobile devices, especially iOS, than any other mail provider.
- The device can only receive what the mail server sends it. There is no known issue of the mail app randomly pulling Spam or Junk mail labelled items into the inbox.
I would try elcpu's suggestion.
POP is also more trouble than it is worth when accessing mail from multiple devices. You might want to consider converting it to IMAP or if that isn't possible, finding an IMAP provider.