Beam Weapons, no, but Torpedoes, yes. Even the most advanced computer possible is STILL only making an educated guess when a ship is performing erratic maneouvres. And the Torpedo STILL has to compensate for the Evasive Maneouvre. The computer CANNOT do that.
And no, the charging of a Torpedo does NOT include the loading of matter or anti-matter. It is already in the torpedo. What is charged is the Torpedoes Power System, which is needed to power the computer, the detonator, the guidance system, etc. The Explosive Power is already there, but it's in a very secure setup which means they do not mix, otherwise they would explode in the torpedo bay. By charging them before firing, you ensure that nothing goes wrong with the detonation system while it is being transported, or even just in storage.
You'd need something vastly more sophisiticated to confuse a computer at that level of technology. A computer that advanced is not going to track a ship, then suddenly pick it up in a completely different location. It would automatically KNOW that something was being used to disguise the location of the target and would be able to either compensate for the confusing element to re-locate the ship. Or estimate the ships location based on previous position and trajectory.
The only way you could possibly confuse a computer that advanced is via pre-planning. Example would be the Voyager Episode where they use Holographic Projectors to create a "fake ship" - as it was Holographic, it was essentially solid, and it was enough to confuse the enemies computer long enough for them to fire their weapons, giving Voyager a free hit.