The bank’s accumulated losses have come up for manageable levels this year.

‘Come up for something’ means ‘to be eligible for something’ or ‘to be in line or sequence for something’.
Ex. She came up for re-election in June.
Hence, the use of ‘come up for’ in the given context is erroneous. While, ‘come to’, which means ‘to attain, achieve or reach something’, will be an appropriate choice to make the sentence correct.