This could be related to a timing issue in bank feed delivery to your accounting software and CaFE auto-sync schedule with your accounting software.
Before getting into the solutions, there are 2 points to understand system-wise first.
1) CaFE syncs itself with and obtains bank transactions from an accounting software.
2) Banks and financial institutions supply direct feeds to an accounting software but the frequency and the estimated delivery time vary, depending on what banks/financial institutions you have your bank accounts with, and also an accounting software.
CaFE runs auto sync once a day; the auto-sync runs at 2am UTC.
In order to explain the timing issue, for example, let's say you have 2 bank accounts: Bank Account 1 at Bank A and Bank Account 2 at Bank B in an accounting software. And also the data feed delivery time for Bank A to your accounting software is Mon-Sat at 11:30am and the time for Bank B is Mon-Sat at 1am. In this case, if you log on CaFE at 8am, it is highly likely that Bank Account 1 is not up to date yet but Bank Account 2 is. Therefore, you need to manually sync your CaFE once you have confirmed that the direct feed into your accounting software was completed.