In the case of Haute Voltige, it's because of the steel pieces. These don't exist in the official version of the Bubble tileset (including that which Lemmini extracts). I believe some addon graphics exist for the Lemmini version of this style which add the steel pieces, but it would appear they aren't 100% compatible with those found in the SuperLemmini / NeoLemmix versions of this style (which are compatible with each other), as they seem to be slightly oddly placed. Regardless, if you open it as a SuperLemmini level (or even as a Lemmini level, then switch format to SuperLemmini or NeoLemmix via the Level Properties window), the level seems fine apart from this slightly-off placement of the steel.
As for Mountains, I get the same issue as you but I can't notice any such obvious cause - the Validate Level function does report though that pieces 178, 179 and 180 refer to terrain pieces that don't exist in the graphic set; even in SuperLemmini or NeoLemmix formats. Did you have additional pieces in your copy of the Crystal tileset back then, by any chance?
If the level *looks* fine (ie: nothing's missing), you can try using the "Validate level" function (under the Tools menu) then clicking "Fix All". This will remove the culprit pieces. However, I'd think there probably is something missing, since both entrances drop directly into water as-is.