They have a deeply inferior product, fail to catch up to Grab's breakneck innovation pace.
Also, being an Indonesian company, Go-Jek has a disorganized company culture that is not conducive to competing with a lean, well-oiled machine run by Singaporeans like Grab.
I also don't think being an Indonesian company has challenged Go-Jek in any way. Traveloka, Tiket.com, and Go-Jek are one of the most prominent businesses in Indonesia, and they all look like well-oiled machines.
Grabs two co-founders were born in Malaysia and the execs are from all over the world.
Both are very successful companies but from the innovation perspective Gojek is most definitely the leader. You need only look at their offering (dozens of products built in house) in comparison to everyone else outside of china. Their food business is now bigger than the ride sharing for example, and their rollout of this was exceptional. Light-years ahead strategy wise of the rest at the time (grab/uber).
The only thing I can think of that Grab has executed on better is international expansion and the initial grab-car service was at one stage far more popular than go-car.