Yes, there is a Frontex delegation in Malta right now
The initial reports this morning, shortly after the Luqa airport crash, were that Frontex personnel were aboard. Frontex immediately tweeted a denial.
It is not clear where this information came from, but there most certainly is a Frontex delegation in Malta today. They were at the army’s headquarters all morning and ate lunch there too.
Informed sources tell me that this very aircraft was used “frequently” by Frontex and by “French observers”, so airport personnel may simply have associated it with Frontex and made that assumption when speaking to the press in the aftermath chaos.
But the most likely explanation is that somebody knew two separate facts – that a Frontex delegation is in Malta, and that the purpose of the flight was reconnaissance on smuggling routes – and drew the natural conclusion.