das Manko
shortcoming
A flaw, deficiency, or disadvantage that impairs the value or quality of something.
Das größte Manko des neuen Smartphones ist die kurze Akkulaufzeit.
The biggest shortcoming of the new smartphone is the short battery life.

shortcoming / deficit
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shortcoming
A flaw, deficiency, or disadvantage that impairs the value or quality of something.
Das größte Manko des neuen Smartphones ist die kurze Akkulaufzeit.
The biggest shortcoming of the new smartphone is the short battery life.

'Manko' (shortcoming/deficit) is often used with the verbs 'haben' (to have) or 'aufweisen' (to exhibit/show). To say what exactly is missing, the preposition 'an' is often used, followed by a noun in the dative.
Der Plan hat ein entscheidendes Manko.
The plan has a decisive shortcoming.
The word 'Manko' (shortcoming) for a disadvantage or flaw is mainly used in written language or in a more formal, elevated style.
Trotz einiger kleiner Mankos ist das Buch sehr lesenswert.
Despite a few small shortcomings, the book is very worth reading.
The meaning 'Fehlbetrag' (deficit/shortfall) is specific to the commercial field. Words like 'Kasse' (cash register), 'Inventur' (inventory), 'Lager' (warehouse), or 'Bilanz' (balance sheet) in the sentence clearly point to this meaning.
Der Geschäftsführer war verärgert über das Manko in der Kasse.
The managing director was annoyed about the deficit in the cash register.
mistake / error
'der Fehler' and 'das Manko' can both refer to something negative that lowers the quality of something. 'Fehler' is more neutral and broader: it can refer to an incorrect action, a defect, or even a personal weakness. 'Manko' more often means a shortcoming or disadvantage that harms the overall impression. It often sounds somewhat evaluative, for example with a product, a plan, or a performance. Learners may confuse the words because both point to something imperfect. If you want to say exactly that something was done incorrectly, 'Fehler' fits better. If you mean a disadvantage in something that is otherwise usable, 'Manko' sounds more natural.

Das einzige Manko der Wohnung ist die laute Straße vor dem Fenster.
The apartment's only shortcoming is the noisy street in front of the window.
Frau Krüger hat den Fehler im Vertrag sofort bemerkt.
Ms. Krüger noticed the mistake in the contract immediately.