Money Dashboard Classic can only receive transactions from the banks when they are fully cleared, so although you may see recent items on your online banking they may still be in pending status and not yet available to Money Dashboard Classic.
The Balance History graphs are plotted by taking the current balance and working backwards from the available transactions. In some instances the balance given to us by the bank will take into account recent pending items.
Unfortunately if the transactions are not yet available this can cause temporary plotting discrepancies with the graphs. This should be resolved when the recent items are picked up on refresh. Pending items tend to clear and become available in 1-2 business days, though in some cases can take longer - e.g, transactions made over a weekend/bank holiday, contactless payments, overseas transactions, etc.