Regarding Miranda Tate's reappearance in Wayne Tower

Poor editing or a continuity mistake... Seems like opinions differ. I guess depending on what happens in the off-screen moments... both are possible. That being said, there's several continuity mistakes in the movie, so it may very well be the case with this as well.

Firstly: Continuity mistake. IMDB has this under their 'Goofs' section.

Goofs

Continuity

When Gordon is taken by Bane's men and put on 'trial', it is shown that Bane takes Miranda hostage. However, a later scene shows Bruce meeting Miranda and Fox, neither are hostages. Later still, when he first appears before Gordon, Batman asks where Miranda is, despite seeing her as Bruce Wayne in a previous scene.

IMDB page can be found here.

Or secondly: Poor editing

From the user Vadersville on the empireonline website:

"Bruce sees Miranda when he is brought before Lucius and tells her he'll come back for her. He and Lucius are then taken away with Selina. Lucius and Bruce go off to get him armed up whilst Miranda and Gordon and his men are taken before Crane in the court and sentenced to death by exile. Bane tells the guards to bring Miranda to him and leaves with her. Bruce then rescues Gordon but Miranda isn't there so he asks where she is. Where is the error?"

Page can be found here.

You were right to feel that something is off: The scenes were in a different (and maybe more logical) order in the original script. However, I'll try to prove that the chain of events that's depicted in the film is, at the very least, plausible, and that some of the problem stems from a few misconceptions you had.

What was the scene order in the script?

1. Wayne returns to Gotham and talks to Selina.
2. Gordon and Miranda are apprehended by Bane's mercenaries.
3. Wayne's brought in as a prisoner and meets with Fox and Miranda; Catwoman appears and helps Fox and Wayne escape while Miranda stays behind.
4. Crane sentences Gordon and Bane orders that Miranda is brought to him.
5. Fox and Wayne work on the Bat.
6. Batman saves Gordon on the ice (but doesn't ask where Miranda is).

What was the scene order in the film?

1 (Wayne's return) and 2 (Gordon & Miranda's capture) are rather followed by 4 (Gordon's trial and Bane summoning Miranda) and then a separate scene we'll call 4b (Blake contacts the trapped cops), then scene 3 with Wayne, Fox and Miranda and finally 5 & 6 with a few minor changes.

Why would that still make sense?

First, a few corrections that might make things clearer:

• The scenes you mentioned do not take place in Wayne Tower but rather in the abandoned Stock Exchange; this is verified by the script and by going over the Stock Exchange heist scenes earlier in the film. Remember that Bane's men control an entire city, after all.

• Fox and Miranda are prisoners in scene 3. It's not for nothing that a captured Wayne is brought there. This is basically a prison yard: The prisoners can walk about but are guarded by armed men and the halls are barricaded.

• The scenes don't happen in real time and don't necessarily follow in immediate succession. Note, for example, that scenes 4 and 3 in the movie are rather separated by scene 4b which would suggest a passage of time.

Bearing these in mind could lead to a more or less plausible chain of events: Miranda and Gordon are captured and Gordon is sentenced to death. Bane asks for Miranda (probably just to check with her or talk strategy, since they're in cahoots) and Gordon awaits his execution. Miranda is presumably then released to continue her role as a mole, this time as a hostage imprisoned with Fox. A little while later, Wayne arrives and, with Catwoman's help, escapes with Fox, promising Miranda he'll be back for her. He gets his Batman gear and comes back to save Gordon. Miranda is seen back with Bane later after he orders to keep her close, knowing that Wayne will go after her.

But why would Batman ask Gordon where Miranda is?

Because he couldn't find her. Since both Miranda and Gordon were held in the Stock Exchange, Wayne figured Gordon would know, but he's mistaken and between them, Wayne saw her last.

According to IMDB (on their "Goofs" page for Dark Knight Rises), comicbook.com, and chaoshour.com, this was an actual mistake, and not just a clumsily attempted time jump/flashback. And I haven't found anywhere that explicitly explains why the scene wouldn't be a continuity error. That said, there are plenty of articles & videos out there dedicated to pointing out the movie's mistakes that didn't seem to notice the discrepancy. Still, I'm personally inclined to say it was a mistake, especially given that I can't seem to find an explanation anywhere.