The latest stable build (r13783) changes the way ship attacks are handled in the tactical UI.
If you have multiple ships selected, weapons now default to firing in batches, rather than one at a time. I'm hoping that the UI and associated behaviors for this are relatively intuitive and easy to figure out, but, the underlying mechanics can get a bit complicated.
For example, batches of beam and kinetic weapons will fire as a group, but, if you have, say, 6 ion cannon mounts selected, and attacking with the first 4 is sufficient to destroy your target, only weapons 1-4 will fire -- you'll be able to use the last 2 on some other target. (Point-blank missile attacks work the same way.)
Experienced beta testers should be aware that some of the core tactical mechanics have changed in subtle ways as well. For one thing, it is no longer possible to fine-tune the number of attacks used by a given mount. Given the new hardpoint setups, this feature isn't as useful as it once was -- and I think specifying attacks on a per-mount basis is already a sufficiently fine degree of control.
EDIT: As or r13794 (now on stable), you can cycle through weapon groups using TAB.