In Saturday's sprint race, Alonso was given a 10-second penalty for a glancing collision with Ferrari's Carlos Sainz towards the end of the race, which resulted in Alonso retiring with a puncture.
The next day Stroll received a similar penalty for crashing into the back of RB's Daniel Ricciardo under safety car conditions, which caused terminal damage for the Australian and also damaged Oscar Piastri's McLaren.
Having judged the steward's swift penalty decision for Stroll as "very harsh", Krack went on to say the "stewards have been tough to Fernando and Lance recently".
That includes Alonso's penalty for 'potentially dangerous driving' in Australia, where his extremely early braking for a corner caught out the chasing Mercedes of George Russell, who crashed off in his dirty air.
"We had it in the sprint race, we had it in Melbourne, we had with Lance [here]," Krack said.
"Last time it was the car in front that got the penalty [Alonso] in Melbourne, even without touching. This time, it was the car behind."
Krack pointed to Stroll's first-lap contact in Bahrain, in which he was spun around by Haas' Nico Hulkenberg, as an example of others escaping punishment.
"Lance gets spun around in Bahrain in lap one, has to come back through the field - there's no penalty for the one that caused the collision," he said.
"So, again, we're not super consistent. That's the feeling.
"It is frustrating. On the other hand, everybody's human. Everybody tries to do their best.
"The best recipe is if you have a fast car, and you drive away. Max [Verstappen] has no such penalties. So it's up to us to make it happen."
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The Bahrain incident happened in Turn 1, with it being deemed a typical first-lap incident that the stewards take a more lenient stand towards.
When asked by Autosport if he got the impression Alonso and Stroll are being singled out for harsher treatment because of their respective reputations, Krack replied: "It is interesting you are asking because it shows that you seem to have that kind of feeling as well.
"I think on a general basis, there has been this discussion about driving standards and harsher penalties at the beginning of the year.
"But then you want action in a sprint, yes? And we had action! I thought it was great racing, even if we had the worst end of it.
"Then spending hours with the stewards again... you feel at that point that it is not fair.
"Maybe we sleep two nights, and we'll see it differently. But again, you have an incident [in the race] where people are pushing another car off in Turn 6, and then there is no action.
"Or we had the two Ferraris pushing one another off, not leaving the gap - there was no action. Fernando? Straight away 10 seconds..."
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