The first indication that the doctors, Nemur and Strauss, have ambivalence about the success of Charley's operation comes in "Progress Report 10." Charley overhears the colleagues arguing. Nemur wants to present their "experiment" at a conference.
Nemur: "We've predicted the pattern correctly so far. We're justified in making this interim report. I tell you Jay, there's nothing to be afraid of. We've succeeded. It's all positive. Nothing can go wrong now."
Strauss: "This is too important to all of us to bring it out into the open prematurely."
Nemur's claim that "(n)othing can go wrong" serves as both foreshadowing and irony. It foreshadows the fact that Charley will regress; it is ironic because nothing could be further from the truth.
As the novel progresses, there are hints that the Strauss and Nemur are unsure of the permanency of Charely's improved cognition. In Progress Reports 13, Charley notices Algernon's waning ability to navigate the mazes. Finally, in Progress Report 15, Charley demands to know the doctors intentions and his fate. Nemur admits that they did not know what would happen, but "we decided to risk it with you, because we felt there was very little chance of doing you any serious harm and we wanted to do you some good." Horrifically, for Charley, Nemur tells him that when his faculties fail, he will be sent to the Warren State Home.
In "progris report 3-march 7," Charlie writes: "They [Drs. Nemur and Strauss] said you know it will probly be tempirery. I said yes." This is your first clue that the doctors knew something that they weren't telling Charlie.
After that, there are several places where Charlie is compared to Algernon. The first is in his "motor-vation" in "progris report 4." It's also revealed that he and Algernon have had the same operation. In "Progress Report 8," Charlie reports that, "So far Algernon looks like he mite be smart perminent."
In experimentation, many times, a trial and error approach is used. Reading between the lines, Algernon wasn't the first mouse Nemur and Strauss had experimented on. Chances are, there were several mice that had been made smart and then regressed. Algernon's intelligence appeared at first to be permanent, and thus, things were hopeful for Charlie. However, when Algernon bites Charlie on May 23, he realizes that his connection to Algernon manifests itself in more ways than motivation.