This also affects mobile but it's an old school runescape bug and didn't see a bug reporting thread for old school itself so this is the closest that comes to what I need to say.
So I was working on my woodcutting and I got a cluescroll nest that was beginner, I clicked it to get the scroll out of the nest but the nest disappeared. I thought maybe you don't get it from them.
Then later on I got a hard one and I got both the empty nest and a scroll.
Conclusion: The beginner cluescroll nest is bugged or just an oversight that was meant to give both a scroll and empty nest.
same happened to me on the client, but from bird houses, every time I receive a beginner clue nest, I get the clue but not the bird nest. this does not apply for higher tier clues, since I recently received an elite clue nest, and I did receive the nest.