I've seen the glitch on other maps too. The easiest way to reproduce the 'disappearing glitch' is to place armies of 8 around a city, attack but only dominate a unit and then leave the fight without losing any of your units. Bam! The dominated unit will be placed onto the same hex as one of the army of 8. During that turn you can select both groups (click on that hex multiple times to cycle through which group you want to select, much like an army sitting on a city). When you end your turn, one of the parties will permanently disappear. I suspect the creators were aware of the glitch on release because they disabled the ability to cast summon spells during combat (which would have also lead to this condition). I'm not entirely sure of all of the conditions that will cause the glitch.

My experience on Xelm was when I was splitting a party (boat + army) to conquer a gold mine and attempted to recombine the party. Two parties overlapped. I recognized what was going on, move my army back to the goldmine, repositioned my boat one hex over and successfully recombined the party following that. It might be caused by the split party / recombined party over a conquer location (hidden autocombat effect?), or it might be the number of independents on the map and something with how the save states are handled. Xelm has a lot of charm and it would be a shame to strip away from it without knowing for sure what the cause is!

One of the neatest elements of Xelm so far (especially compared to the earlier release) is the wide range of heavily defended locations that forces decision-making for where to start to expand. I think starting with a transport ship is great too for its ability to block other transports from entering your territory and that adds a whole new dimension to the game I haven't seen in any other map. So far the only tweak I would give to the map is a bit of starting gold to reduce the idle time (but not too much because scarcity forces the player to pick and choose which friendly mercenaries to hire). If you're worried about the glitch, I think it would be better to try to reliably reproduce the glitch and then experiment with map design to see what makes it tick.