Noggit SDL 1.4 - Assist menu, Fix gaps (all adts) function.
In case you don't want or can't use this function (f.i. if you use older version), simply use flatten tool. About those holes, do NOT click/draw over those holes. Use flatten tool only around boarders of holes, since when you click into them, noggit targets with your tool place far behind your intended area, which leads to creating those holes.
Just btw, this can happen also when you are just modelling and some gaps creates as bug in your terrain and you click on it/draw over it. It tends to happen around chunk boarders, so I, in general, recommend to be careful even when just modelling around chunk/adt boarders.