Mercedes had topped the weekend's opening session through 2016 race winner Lewis Hamilton, but slipped down the order in FP2, with Bottas 10th and Hamilton eighth.
As they did so, Ferrari hit the fore with Sebastian Vettel while Red Bull also surged forward, with last year's polesitter Daniel Ricciardo emerging as Vettel's closest challenger.
"I hope [the deficit] is not real," Bottas told reporters afterward. "We made some changes for FP2, some mechanical changes, and went in the wrong direction - Lewis as well. We definitely struggled.
"We know how to fix, but other cars are looking good as well.
"We can't be too happy as a team with P8 and P10. Everything was looking okay from FP1, but we tried to help the balance and went wrong. We adjusted at the end of FP2 and it felt better, but the tyres were old by then.
"So we learned a lot - but we need to work hard to come back to the front."
Hamilton said the extra day off before qualifying on Saturday could work in Mercedes' favour, adding: "Something just went wrong this session and we have to figure out why.
"The car is handling fine, particularly this morning - but this afternoon we couldn't get the tyres working. The extra time gives the guys more time to work on the car."