I couldn't understand 入ってなかった, what verb is it after 入って?
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入ってなかった is the negative past form of 入ってある. The -てある form is used to indicate that "something has been done to something and the resultant state remains" (from Makino Dictionary of Japanese Grammar). The translation of your sentence would be:
So, when you came back the phone was missing from your bag, right? (implying that someone took it)
Here's an example to understand the difference between -てある and -ている:
窓が開いている -> The window is open. (no agent or reason implied)
窓が開けてある -> The window is open (because someone opened it).