Кроме того, выявлены отдельные недостатки в части осуществления контроля за функционированием средств защиты от вредоносного кода на рабочих станциях...

Besides (in addition), we discovered that the Bank did not exercise proper control over the functioning of malware protection systems on work stations...

...

Вот, кстати, к вопросу с соседней ветки: как это переведет переводческая программа?..

...выявлены - we have found that...

'Shortcomings' is a good word to use here:

'In addition¹ we (discovered/found)² (certain/specific) shortcomings in the way the (bank/Bank) (exercises/exercised)³ control over the functioning of malware protection systems on workstations⁴ '

¹  'besides' is slightly more informal than 'in addition', so I would play safe here and say 'in addition'.
²  or 'have (discovered/found)', depending on the tense.
³  depending on the tense.
⁴  Most people tend to write 'workstations' as one word nowadays when it refers to computers, although 'work stations' (as two words) will be clearly understood.