some of that is bound to happen around structures, especially when one profile may be low flow, and the next pressure flow. Or pressure flow to pressure and weir flow. Switching between equations (which is what RAS does when switching between these regimes at bridges) can cause some overlapping of profiles just upstream of the structure.
This can also happen when ineffective flow areas are just “overtopped” and turn off. Again, this should be a local phenomenon.
Sometimes, it’s numerical instability. I suggest plot critical depth and see if you are defaulting to critical depth as some of the “jumpy” areas. You may need more cross sections, or better cross sections in these areas.
Good Luck-
Chris
@RASModel