It´s a bug that happened to me a few times where 
E stopped 
R. When I used R he E away canceling my ult. My R sounds played, the voiceline (Battlecast Skarner) played but my R didnt go on cooldown nor did Ez get suppressed. I knew about Skarner R vs Trist R (pulling her with you) but that was something new to me.
VarysPeter1 votesThis is due to different abilities being coded different ways. Skarner is (let's face it) an outdated champion, and Riot never made the effort to correct these types of interactions, just threw him in the "one-day-we-might-rework-him box".
Rouwhorst1 votesThe Skarner ult suppress has at least a cast time after which it checks again if the target is in range, if not it fails. The audio clue is probably timed to be at the beginning of the cast time. This they could change! Quick movement like a flash or Ezreal E during the cast time make the ult not go trough.
Looking at the wiki they mention an approximated 0.25 second root before the actual suppress comes through. (no idea if this is true) A root stops movement and disables the casting of movement abilities. Yet, it does not interrupt mid-dash or an ability's cast time. So if this is true it is also possible for certain champions with long cast times on quick mobility skills (ezreal E, perhaps Ekko E or trist W) to escape the ult during the rooting phase too.
The reason that it checks again is probably because it otherwise caused some even more terrible situations for others. A quick search gave me this video, showing skarner ult someone who flashed away during the cast time of the ult, but due to the absence of the second check, the target is pulled all the way back even though he used flash to get away.
Mael Jade1 votesWell, I already ulted a 
who tried to ult me away and she got pulled with me :D
Rouwhorst1 votesThat is a different scenario. If the skarner ult is already connected, it won't (easily) break loose. During the windup and the root trist can still fire her ult. But it has a cast time and travel time meaning it will be heavily delayed and if used after skarner started casting the ult, the suppression will have started already before he is knocked back. If the skarner did get knocked back before the suppress came trough then, yes, it can fail in this situation too. The same can be done with poppy's R.