Tech maps are notorious for this, because of the way the elevators link, sometimes the fourth layer of the mission is actually in the middle of the map simply because the way the play area was laid out. It makes it hard to plan accordingly. Experiment and test a lot until you can work something out is what I had to do.
No tech maps here. The culprits are the Vaults of MU oranbega map (coolest map in history, just for the record), and the Ruladak's Cave map. Both are single story, although Ruladak's cave has an admitedly unorthodox shape, being a large spural with many small stuck in every which way for the sake of confusing the player.
Also, this is an unrelated question, and one I fear I know the answer to, but is there any way to test a single mission without running through the entire arc? Since these are the last 2 missions in a 5 mission arc it would be nice not to have to play through the first 3-4 missions (the first 3 of which work perfectly) every time I make a single minor adjustment and want to see how it plays out.
You can pull the mission to the first position (they're drag and drop) and just test that one. Then put it back when you're done. This isn't readily apparent until someone tells you.
Dec out.
Something I'd really like to see to alleviate this issue is being allowed to pick a particular spawn point for your objectives. I'm not talking about exact coordinates, but perhaps an actual list(simple numbered dropdown would be fine) of all available spawn points in the map, so that we can place our boss or glowy or patrol or whatever at that same location, every time.
Id like that too, KYasubaru. Unfortunately the developers dont seem to feel we're worthy of that ability (and I know the capacity to do it exists, because there are developer created missions where something /does/ spawn at exactly the same location every single time).
Aside from alleviating this problem this would give me the oppertunity to get my archvillain "fight a boss" ambus to spawn on top of the players like its meant to as supposed to half a map away. But I digress...
Decorum, you are officially my savior! Thank you!
I've never encountered that, but they could simply accomplish that by having extremely limited spawn points on the map in question. If there is only one spot for collect items to be placed, they won't move from it.
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Id like that too, KYasubaru. Unfortunately the developers dont seem to feel we're worthy of that ability (and I know the capacity to do it exists, because there are developer created missions where something /does/ spawn at exactly the same location every single time).
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Rather then them not feeling we are worthy of the ability, think of it as more like, how many more months did you want to wait to get it in? Perfect is the enemy of good enough, and they needed to get it good enough to get it out. Now they can datamine how things are working, find and fix the bugs that were hidden until it was stressed by real world loads, and add more features in future Issues.
Now we have an MA that we can use to tell some great stories, with the promise that it will get better. Because they know we want this stuff. Believe me, it was mentioned many times before Beta was opened up. Just don't irritate Positron too much, or he might give us the cut scene generator with its current user interface. 
Justice Blues, Tech/Tank, Inv/SS
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Fighting The Future Trilogy
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Mmm, a cut scene generator would be /awesome/ no matter how bad its interface is.
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Something I'd really like to see to alleviate this issue is being allowed to pick a particular spawn point for your objectives. I'm not talking about exact coordinates, but perhaps an actual list(simple numbered dropdown would be fine) of all available spawn points in the map, so that we can place our boss or glowy or patrol or whatever at that same location, every time.
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The downside is that this will be yet another thing to take up file space in an already crowded 100KB.
Im sure (or at least I hope) I cant be the first to ask this, but is anyone else having trouble getting non-boss objetives, notably item retrieval and ally rescue objectives, to appear in the proper part of the mission?
I have observed that in particular items and allies set to "front" tend to spawn not only towards the end of the mission, but IN THE FINAL ROOM! A significant inconveniance.
Sometimes reversing the order (front to back) seems to work, but sometimes it does not (I'm having a murderously hard time making things work properly on Ruladak's Cave Map.
Curiously boss encoutners do not suffer from this problem.