As shown in multiple EU sources, a tractor beam locking on to a small craft can easily be countered by having another small craft fly at a right-angle between the source of the beam and the captured craft. It is also possible to use a missile or debris field to break up the tractor beam. I would offer sources, but there are far too many to choose from.
We see this technique, known as the Covert Shroud Manoeuvre, was used early as Timothy Zahn's Heir to the Empire, where Luke Skywalker uses a proton torpedo to escape the tractor beam of Grand Admiral Thrawn's flagship, Chimaera. He changes his speed so radically that he temporarily escapes the beam, which is depicted as not being uncommon; a tractor operator would normally just latch on again. On this occasion, however, the tractor operator locked on to the torpedo instead, which both enabled Luke's escape and had the added bonus of damaging the Chimaera when the torpedo exploded in a docking bay.
The CSM was used by Han Solo on multiple occasions, and he seems to be the undisputed master of the technique. Luke may have even learnt of the manoeuvre from Han; the narration in Heir to the Empire states that Luke has "heard of this working at least once before," but it never states from who. Luke was onboard the Hand of Judgement's modified Suwantek freighter when Han and Chewbacca used a destroyed TIE Fighter as a shroud during the events of Allegiance, so that may be the incident he is thinking of.
Han Solo also used the CSM during the events of The Paradise Snare, escaping an Imperial Corvette orbiting Ylesia. This incident showed both that the manoeuvre was known amongst the galaxy's smugglers - it was a fellow spice-runner who assisted Han in executing the manoeuvre by flying between Solo's ship and the Corvette - and that the Empire had encountered it before the Battle of Yavin.
With a large number of small fighter craft to combat, using the tractor beam in combat would have been counter-productive. There was always the chance of accidentally latching on to your own craft, the enemy could easily use the CSM to escape any beams that were established, and using the tractor beams in such a situation would only serve to highlight them for any enemy wishing to take a pot-shot at an important piece of equipment.
I know of only two incidents off the top of my head of a tractor beam being used in combat for any purpose other than pulling an individual ship - or a few small ships - into a docking bay, or holding them for destruction. The first was during The Thrawn Trilogy, when Grand Admiral Thrawn had a damaged vessel, with no guns capable of hitting the Chimaera, used as a kind of living shield against any enemies attacking an area where the flagship's shields had failed. The second was when Errant Venture was held in place by multiple tractor beams during its raid on Yaga Minor in Vision of the Future; even then, it was a single ship inside the base while the main battle took place outside. Thrawn, and therefore his part-clone Grodin Tierce, had a bit of a thing for tractor beams that was not shared by most Imperial officers, which might explain why the former tactic was not a common one. It would certainly have helped Admiral Piet and the Executor survive the Battle of Endor.
In addition to this, the Death Star itself may have needed to use its tractor beams to protect itself from the debris of the planets it destroyed, though this is merely supposition on my part. Destroying a planet is going to create a lot of debris; in A New Hope, it created a new asteroid filed in the Alderaan system, which the Millenium Falcon proceeded to fly into. Some of this debris could potentially damage the Death Star. That's a good reason not to risk the tractor emplacements in combat. And, of course, once the Rebels were past a certain point, they may well have been too close to the station itself for tractor beams to reach them, much like flying too close for the heavy turbo-lasers to hit.
I should point out that as of the events of Spectre of the Past, the CSM is no longer effective against Imperial Star Destroyers, as Lieutenant Mithel works out a method for countering it between the events of The Last Command and this book. Mithel was hand-picked for the purpose by Grand Admiral Thrawn, after Luke Skywalker used the technique to again escape the Chimaera in The Last Command.