Goalkeeper Ann-Katrin Berger and midfielder Drew Spence missed the game due to positive tests as Chelsea were knocked out on goal difference after finishing third, level on 11 points with Juventus and group winners Wolfsburg.
A number of Chelsea players were unable to go home for Christmas last year after a Covid-19 outbreak in the squad.
Hayes said there were 20 positive cases last year and that she fears Chelsea will be in the same position next week.
“Our heads were all over the place, we are human beings,” Hayes said. “A few days ago we had two players stuck down with Covid, we know inevitably that when we land tomorrow there will be positive cases.
“When you are in a team environment, you know it spreads like wildfire in the team.
“I just feel that this was deja vu and we are here 12 months after a really bad Covid outbreak at the same time. It’s across the game at the moment. For me it’s a major reason behind performance tonight.”