Our "regular" magic-based dots will stack with each other. These are the ones we get on the 1's and 6's (ie level 71, 76, 81, 86, etc.). Spells like Beetle Swarm, Scarab Swarm and the like.
There is another magic-based dot that was introduced to us in SoD called Swarm of Bees at level 83. This one does not stack with any higher/lower versions, acting the way you described by not landing and/or overwriting.
At 95, I have my swarm dot memmed 98% of the time, and have my highest and second highest other 2 dots memmed when I don't need those 2 spell slots for utility.
So basically, you can have your highest level dot and the one from the previous expansion and should have no problems landing them. It works this way with our nukes too, except for them it's because of spell types coded into the spells themselves.
Now at lower levels (before they gave us the same cookie cutter spells every 5 levels) the stacking issues may still be there. When I was using those spells I didn't have the benefit of extra spell slots, so I hardly ever used a lot of dots... but I do remember being in my 50's killing hill giants with root rotting, and stacking about 3 dots on them at once (as weak as my dots were, lol), and I didn't have any stacking issues then.