Basically, the probes were both 386,000 km (240,000 mi) farther from where existing models predicted they would be. This came to be known as the “Pioneer anomaly“, which became common lore within the space physics community. While the Pioneer anomaly was resolved, the same phenomena has occurred many times since then with subsequent missions. As Dr. Acebo told Universe Today via email:

“The “flyby anomaly” is a problem in astrodynamics discovered by a JPL’s team of researchers lead by John Anderson in the early 90s. When they tried to fit the whole trajectory of the Galileo spacecraft as it approached the Earth on December, 8th, 1990, they found that this only can be done by considering that the ingoing and outgoing pieces of the trajectory correspond toasymptotic velocities that differ in 3.92 mm/s from what is expected in theory.

“The effect appears both in the Doppler data and in the ranging data, so it is not a consequence of the measurement technique. Later on, it has also been found in several flybys performed by Galileo again in 1992, the NEAR [Near Earth Asteroid Rendezvous mission] in 1998, Cassini in 1999 or Rosetta and Messenger in 2005. The largest discrepancy was found for the NEAR (around 13 mm/s) and this is attributed to the very close distance of 532 Km to the surface of the Earth at the perigee.”