A non-event made into something by misleading media headlines.
Yes it was a military charter, however outside Kabul FIR it uses a civilian call sign by a UAE airline that regularly flies through Iranian airspace on a daily basis.
A paperwork mix up which meant a delayed flight plan wasn't updated. The Iranians even gave the aircraft pre-clearence to enter their airspace, and it flew pretty much through the entire FIR before they asked it to either exit via the point it had entered or land at an Iranian airport to file the correct paperwork before being released again.
It was on the ground for an extended period because the crew after being delayed were at the limit of their allowed flight duty time.