You were not confused. The writing was wrong and the counting was ambiguous, and between them they described an app that does not exist.
Nothing lands in the Inbox folder. Ever. You are exactly right, and the Field Guide said otherwise about all three kinds of capture:
Web clips go to your clip folder — Clippings, unless you renamed it in Settings ▸ Web Clipper.
The Bucket appends to a page called Bucket, which it creates the first time you use it.
Files you drop in stay where you dropped them.
That sentence is the one thing a new reader trusts about capture, and it was false three ways. It now names the three homes, and says the thing it was actually reaching for: nothing asks you to file at the moment of capture, because deciding is what interrupts thinking.
Now the part you found next, which is the more interesting one.
“Inbox” in MojoPad is not a place things get put. It is a view of everything you captured and have not filed, and it looks in two places: any folder you have called Inbox, and your clip folder.
So what you saw is exactly right and not a fault: the Inbox folder can be completely empty while the inbox card shows a count — because the count is your clippings. Nothing is lost, nothing is miscounted, and the folder is not broken. The card was simply looking in both places and only naming one of them.
I have fixed the naming rather than the behavior, because the behavior is right and only the words were hiding it. The review step now says which places it gathered from, in its heading and when it is empty, using your clip folder’s real name so it stays true if you rename it. The manual now states the empty-folder case outright, so the next person to notice it finds it written down instead of having to work it out.
One thing I left alone deliberately, and it is worth knowing since you clearly poke at these things: if you have no folder called Inbox at all, the card never appears. That is on purpose — otherwise an update would turn a Clippings folder somebody has kept happily for years into a pile of homework overnight.
Both fixes are in the next update. Thank you for pushing on the second one; the first was a documentation error, but the second was the app being unclear about its own idea, which is the more useful thing to have had pointed out.
Mark