First of all, the authorities were surprised that so many people came to Navalny's grave despite the obstacles. If you consider the number of residents in Moscow, the number of people mourning Navalny publicly is not too large, but apparently the current master of the Kremlin also knows how many mourners there were who did not come out on this occasion.
Second, the Kremlin knows what the election results actually were. There were «noon» actions, where people went to the polling stations at the same time, and some definitely ruined ballots as well. According to official data, support for Putin was 87 percent, but the president's administration is still summarizing the real picture. It is likely that Putin did actually receive a large share of the votes, but evidently the amount of so-called votes against was surprisingly large.
Thirdly, the considerable number of actions organized at polling stations was surprising. It was not on a large scale considering the size of Russia, but compared to before, it was significantly more numerous and visible. Moreover, the authorities know how many such actions the FSB prevented.
The fourth reason is undoubtedly the events around Belgorod. One region is sinking out of control, and although Moscow will probably restore its power monopoly there in the coming days, it is still a «bad example» for other regions.