[OmikronWarrior]

Indeed, as archaeolept suggests, stopping them may be a lost cause. Instead, you have to kill them after they land. There are numerous ways to accomplish this depending on the thug/SC you need to nullify. For example:

Kill spells such as Seeking Arrow, Mind Hunt, and Vengeance of the Dead can make a well equiped thug very cost inefficient.

Anti-thugs, or units designed and equiped to quickly kill thug/SC chasis and little else, are also effective counters, especially if they can cast Teleport or Cloud Trapeze. These spells move units in the "magic movement" phase, which occurs before the normal map movement phase, and results in a battle before the SC or thug can move away.

Finally, guessing where the thug or SC is going to move behind your lines and putting an army there can work, though obviously is not as efficient.