I recently rewatched The Prestige and find this question to be central to understanding the plot. In the final narration Cutter seems to be challenging the audience to discover a further, hidden secret. This secret would necessarily not be made explicit in the movie, but nevertheless be key to understanding the entire plot.
I think it is possible that Angier did not know that Borden was backstage. Angier had planned all along to stage his death after 100 shows, so that he could return to being the Lord full-time. Perhaps he also realized that he could not go on murdering himself indefinitely, so he put a hard limit on the practice. Borden's presence backstage was therefore a coincidence.
Another possibility is that Angier did know Borden was there spying, because Fallon had told him. After Sarah's suicide, Fallon secretly wanted his twin brother dead. Possibly he involved Cutter in the scheme at some point. Then Fallon killed the Lord in order to retrieve his daughter, whom Angier did not realize was actually Fallon's.