I did know that Transformers and My Little Pony shared some names, as they are both owned by Hasbro but after doing research, I find out that Transformers share more names with G.I. Joe. According to this All Wiki page, they share about 85 names. According to the same page, MLP and Transformers share 15 names, but some are a bit of a stretch as it isn't the exact name. For example, there is a Transformer named Scoop but in MLP there is Sweet Scoops and Sweet Cream Scoops. Here are some that have the same exact names:
The G1 Autobot was a beach buggy. G1 Beachcomber for MLP was a sea pony and the G3 Beachcomber is a pink Earth Pony with a flower. G1 Autobot appeared on the Transformers TV show and G1 Beachcomber sea pony appeared on the original MLP show.
Seaspray was an European Seapony and G3 Earth Pony and Seaspray has been in many incarnations including G1, Transformers Animated, Transformers Prime and a hovercraft in the live-action movie series.
Zigzag is a G1 Decepticon that becomes a gun, no version of this character or mold was released in Japan. Zig Zag was a G1 Zebra Pony Friend. Neither did not appeared on any of their respective shows.
DJ was a maximal from Beast Wars 2 Anime in Japan. DJ was a background unicorn in My Little Pony: Friendship is Magic that the fans gave a name to and soon will get a toy.
Decepticon Triggercon of G1, appeared in the US and UK comics with a toy in 1988. Windsweeper is part of the Dream Beauties of 1989-1990. Both appeared after the cartoon series.
NightGlider is a G1 'Twice as Fancy' Pony and NightGlider is a Maximal from beast Wars who was only a toy (Transmetal 2).
A G1 Targetmaster and a G1 1983 unicorn, both did not appear in cartoons.
From the G1 cartoon and special monthly ponies in G1.
G3 Pegasus (two different distinct versions) and part of Astrotrain from G1.