The movie goes to great pains explaining the notion of experience versus reality within the context of 'The Matrix'. As such we know that there is literally no pill; they do not exist. I guess it can be thought of as a 'sudo' for the trace program? Either way, I don't believe anything is actually being initiated from or by the pill as we understand things. The operator is the one actually executing the program. Why would the operator choose to run a trace program and put someone to sleep? Just because Neo could potentially decide to take both pills?

Robot 1: hey why did the server crash and what happened to all the humans. Other robot 2: eh looking at the error console it seems one of the humans ingested to contradictory virus pills causing a feedback loop that crashed the matrix servers and life support. We can turn the servers back on but there's really no point without the humans. Robot 1: welp guess we could try going nuclear. Robot 2: you crazy your gonna kill us all with radiation not to mention the environmental damage just think about the tree matrix.