Has there been a fight where someone with a much lower BJJ skill set got an unexpected submission on someone who is good or known for their BJJ skills. 
Frank Mir (purple belt at the time) vs. Roberto Traven (world champion black belt)
RogerThatMMA - McGeary vs OrtizHa
I wouldn't say it was unexpected because...well it's fedor but his armbar on Coleman came out of fucking left field
Inverted Cracked Skull -Tito does have an under rated ground game. He almost caught Machida in a triangle when Machida was still on his way up. But at this point, I wouldn't say it was surprising.RogerThatMMA - McGeary vs OrtizHa
TheDigitalRuler - Frank Mir (purple belt at the time) vs. Roberto Traven (world champion black belt)
I remember that fight. Frank used GnP to set up a perfect straight armbar.
Hughes choking out Big Dog Almeida.
PeterIrl - Hughes choking out Big Dog Almeida.Hughes was even surprised.
Chonnan vs silva. I don't know what rank chonnan was but that sub came out of nowhere.
Mackens Semerzier triangles Wagnney Fabiano in two minutes
Lebens triangle on sexyama 
josh burkman sub over jon fitch. burkman has always had great bjj but fitch has always been hard to sub even for Demian Maia who fought him before that match.
FFTF_stuffadamdoes -I remember Rogan saying you have to be strong as fuck choking someone out from the top position like that. That's all arms...PeterIrl - Hughes choking out Big Dog Almeida.Hughes was even surprised.
Forrest Griffin subbing Shogun in his UFC debut.
And before thiaguy goes nuts, yeah yeah, bad knees, not the real Shogun, etc. Point is, no one saw that coming.
Nobody expects the Spanish Inquisition!
TheDigitalRuler - Frank Mir (purple belt at the time) vs. Roberto Traven (world champion black belt)
this was my first thought as well
Anderson tapping out Lutter. Goldberg was shocked
Jim Miller subbing Fabricio Camoes.
Jones vs machida
Jones vs victor
Pettis vs Henderson
ShakaSway - Anderson tapping out Lutter. Goldberg was shocked
Well Lutter is the Michael Jordan of BJJ after all.