2nd takedown mission to the same settlement and guards immediately hostile ?

I completed a standard takedown mission successfully, not spotted \ no alarms and took the Apex back to the starport.

I then picked up a second takedown to the same settlement and took another Apex. I was hopping from roof to roof looking for target\clear terminal when a guard, outside the red map circle when hostile and settlement alarms triggered.

Wasn't targeted for a scan, no bounty etc so not sure why.
Is there a cooldown period ?

Update: Another Cmdr mentioned that you can get a message that the base is on alert, this may have been the case and I missed the message
 
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