You are right in your assumption that it was caused by the gravitational anomalies in his house. More precisely, it was the very slight gravitational time dilation caused by the anomalies. This interfered with the tractors' GPS, since the working of the GPS relies on the satellites accurately accommodating for their time dilation with respect to the time on earth's surface, such that minimal deviations from that time dilation can confuse the system and result in errors. This is mentioned to some degree by Cooper after fixing the tractors when he says:
I had to reset every compass clock and GPS to offset for the anomaly.
So it was the GPS that was somehow wrong, even if Cooper didn't know the exact cause yet.
This explanation is also supported by Kip Thorne, the astrophysicist who co-produced and advised the movie from its earliest conception onward, in his book The Science of Interstellar, where he writes
[The GPS] would fail if the signal transmission times were the true time measured on the satellite. Time at 20,000-kilometer height flows more rapidly than on Earth by forty microseconds each day, and the satellites must correct for this. They measure time with their clocks, then slow that time down to the rate of time flow on Earth before transmitting it to our phones.
The GPS system that Cooper has adapted to control harvesting machines, as they roam through the fields, has also gone haywire, and a bunch of harvesters have converged on his farmhouse. He attributes this to gravitational anomalies that screwed up the gravity corrections that any GPS system relies on.
And in this way this incident directly ties into and foreshadows not only to the prominence of gravity in the film's story, but its effect on the passage of time specifically.