During Pres. Eisenhower's terms in office, the best-known covert operations were the ones that led to the overthrow of the governments of Mohammed Mossadegh in Iran and of Jacobo Arbenz in Guatemala. This sort of operation worked in the short term, but often came back to haunt the US. The Iran operation is perhaps the best example of this.
After overthrowing Mossadegh, the US supported the Shah of Iran as ruler of the country. The Shah's government, however, was autocratic and repressive. US support of such a government led to hatred of the US among many Iranians. This hatred manifested itself most clearly in 1979 when Iranian revolutionaries overthrew the Shah and captured the US embassy in Teheran. The bad blood between the US and Iran continues to be a major problem today. These bad relations can be said to have stemmed from Pres. Eisenhower's covert operations.