I'm sorry, what do you mean by this exactly?
Generally, I'm launching apps directly, i.e. calling Alfred by cmd+space and typing the name of the app. However, in the situation we're talking about, I noticed that they do not appear in the results until I open them for the first time. So if it's the first time I'm calling an app that was just installed, I open it with cmd+space, then another space, so I get the apostrophe in the search bar, as if I'm searching for files. This is what I do and this is what causes the issue, I reckon.
Is this what you meant?