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"We have already let the United States know that this is an issue that appears to be seriously at fault, and we will be making a formal protest if it appears that that is what has happened," she said.
"There's embarrassment about the fact Britain might have been used as a staging post and annoyance at the fact procedures don't appear to have been followed.
Prestwick - which lies 30 miles south of Glasgow - had supplied logistical aid for military flights since WWII in "moving troops and cargo", an airport spokesperson said.
"That support involves allowing crew to rest, refuelling aircraft and providing food and water.
"The airport is obliged to allow aircraft from any CAA-registered country to land here."