Space Mountain, more than pretty much any other attraction in WDW, is more succeptible to "cascade" E-stops.
The way that the ride's blocking system is designed, each rocket only has a short period of time that it can sit at the unload station. More rockets are constantly coming in behind it, as quickly as every 21 seconds if running at full capacity. There are brake zones before the unload station that rockets can be held at, but if a rocket sits at unload too long the system eventually runs out of parking places and the ride has to stop cars that are still out on the course. At that point, the stoppages cascade backward through the ride until the ride comes to a stop.
It doesn't even have to be a single rocket sitting at unload the entire time. A number of slow-to-unload rockets in a short period of time can cause an accumulated delay, leading to the inevitable.
After an E-stop, the other side has to be cycled out, and then both ride systems reset. And while the attraction is shut down, they stop allowing Guests to enter the queue, and the wait time will either go blank or will increase to a large number.
The big refurb a couple years ago replaced the control system, making this reset period a LOT faster (from what I've heard it's a 5-10 minute reset, where it used to be 20-30)
-Rob