Many accounting systems today allow for automatic bank feeds. Where these involve an extra charge people make a choice, but where they're thrown in for free, usually no thought is given to them. In a well-run system where transactions are recorded at the time of the transaction, the benefit is often minimal, but if they are used they add another potential issue.
When bank statements are in your accounting system automatically, bank reconciliations are usually done against it. BUT there is a level of inaccuracy in the bank feeds, often compounded by user error. You MUST check the balance against your bank statement (manual or electronic). If you rely on what your accounting system thinks the balance is, you are likely to have problems.
Bank feeds are never 100% accurate. Years ago accountants pretty much all used Banklink to capture bank statements automatically. Gradually more and more clients used their own systems, and today it is much less common for accountants to code bank statements.
Banklink was bought by MYOB, which means their bank feeds have years of experience. Other suppliers have done various things to improve their systems, but there can still be significant differences. Compare a bank feed with 99.9% accuracy against one with 99.99% accuracy. The difference seems insignificant, but one has an error every 1,000 transactions - the other every 10,000.
The point is, no-one's bank feed is infallible. (I have even seen incorrect bank statements, although only once or twice in so many I can't imagine the total). That is why when you complete bank recs, you MUST reconcile your system total with the bank.