Hate when that happens (LOL)... but it happens.
The reason it happened? Because before staining and finishing, there was unrelieved tension in the wood. That could have been just normal happenings when you take two pieces of wood and align the face surfaces during a glueup... Then when it gets wet, the tension tries to relieve itself... It probably took a slight twist when it did that. When you are in the middle of that, you can pre-relieve some of that by wiping it down with mineral spirts or alcohol, which alos helps clean the pores. Then adjust for it.
Now that it is relieved, It should be fine from now on. Taking it apart to redo it... Might introduce more tension back into it... Then you are going to be going through that again.
The method presented is good. Takes into affect that the workpiece is going to be in the position it is going to be used. There's some other variations of that... but that works. Another is to ensure the surface you measure from is level, then shim the workpiece so the top surface is level. That will keep help prevent that DIY spoof commercial where the guy leveled his own table and the glass slides off it... from happening.
"Don't worry, I saw this work in a cartoon once."
"Usually learning skills and tooling involves a progression of logical steps."