"I thought this story was dead wrong. They already have a partnership. They didn't need to do this deal," Cramer said on CNBC's "Squawk on the Street." "I'm just saying that [Altera's] stock was up for a very long time and I knew that it didn't make sense."
News of a possible acquisition move between the two companies first broke in March, and led to Altera's stock rising 28 percent. The tech company opened Thursday trading down more than 7 percent before regaining some ground, while Intel's stock dipped about 2 percent.
The two companies have not talked in more than a week, according to sources close to the situation. They also said that Intel did make an offer to Altera in the low $50-per-share range.
Altera and Intel did not immediately respond to a request for comment from CNBC.
Cramer added that a deal between semiconductor company Broadcom and Intel would have made sense. "I always thought it was Broadcom; I didn't think it was Altera," he said. "They tried to talk in the 1990s and the deal failed."
Broadcom's stock was up about 1.8 percent in midmorning trading.
—CNBC's David Faber contributed to this report.
Disclosure: Cramer's trust did not own stock in any of the companies mentioned when this article was published.