When I rotateMesh() and clearRotation() of a plane acquired by Primitives.getPlane(40, 1), my vertex shader doesn't work in the proper axis. If I leave the rotation in its matrix, it works fine. That has to be considered a bug, right?
No, why should it? The shader works with the matrices that you give it. In one case, you are working with a rotated matrix, in the other case, you are working with the identity matrix. If that leads to different results, it's an issue with the shader, not with the engine.