Most drivers clocked 23-26 laps during the first hour of running at the Circuit of The Americas in Austin, but Stroll could only complete five tours and team-mate Fernando Alonso was limited to 18 laps.
This will prove particularly costly because Aston Martin is trying to validate an upgraded floor and bodywork, plus the sprint race format means the team now moves straight into GP qualifying.
Explaining the FP1 unreliability, team principal Krack said: "We went out for the first run to check the car basically and we had a bit of an overheating issue on the front-left for both cars.
"We had to come in because we saw we had a fire from the onboards."
After an inspection, it was determined that the damage to Stroll's AMR23 was extensive enough to mean repairs could not be completed in time to get him back on the circuit. Alonso did resume, however.
Krack clarified that the issues were unrelated to the new and upgraded components.
But he urged his team to do better, particularly since the interruptions will further hurt Stroll as he bids to rediscover his confidence in the car after poor form set in particularly following the summer break.
Krack also cited FP1 at Zandvoort and second practice at Monza, where Stroll was twice unable to complete a lap due to power failures, as the team failed to help the Canadian.
In defence of Stroll, Krack continued: "We have not been able to provide a car that is reliable to do the practice sessions that he has to do.… what do you want to do? We have to just get better with this.
"There are also incidences where Lance would say himself, 'I have to do better in here'.
"But, all in all, as long as we cannot provide a consistent car that we can start to learn what you have [with Austin upgrades], honestly how will he go into qualifying now without having done any proper running?
"We need to factor all these things in. We have to do better than this."
