This Time Magazine article from 1 April 2003 asserts that a "handful" have broken up in Iran.
But in the past week, three U.S. Tomahawks have gone missing in the rocky plains of southeastern Turkey en route to Iraq, several hundred miles from the war zone. Five more went astray in Saudi Arabia, and a handful of others have broken up in Iran and, reportedly, Syria.
The article focuses on missiles that have landed in Turkey and is probably key in understanding the difficulty of identifying failed Tomahawk flights. Tomahawks that landed in Turkey or Saudi Arabia were able to be investigated by US officials. However, Iran has had limited diplomatic ties with the United States since the Iranian Revolution. Therefore it would be difficult to examine these claims. In contrast, this article states that US officials were able to examine crashes in Turkey.
In Turkey, angry locals threw eggs and rocks at American advisers when they arrived to inspect one of the crash sites.
Several other articles that I was able to find claim that the US was investigating Iranian claims.
From CNN, 22 March 2003
WASHINGTON (CNN) -- The United States is investigating Iranian claims that three Tomahawk cruise missiles fired by the United States might have missed their intended target Friday and landed in southwestern Iran.
The Iranian News Agency reported missiles landed in the area of Maniuhi, close to the border with Iraq.
Another rocket was reported to have hit near an oil refinery depot Friday evening in Abadan, some 30 miles east of Basra. Eyewitnesses told reporters two guards at the depot were injured in the blast.
The U.S. military is investigating whether the missiles might have gone off course. Tomahawk missiles are fired from submarines or ships. The missiles have a range of 1,000 miles.
So far, State Department officials said, "radar tracks" of the Tomahawk missiles and overhead satellite images show no evidence of an "impact crater" in the area where Iran claims the missiles hit.
From AP (by way of Plainview Hearld), 21 March 2003
Friday's incident was believed to be the only report of a Tomahawk malfunctioning during launch since the war began, though Pentagon officials said Saturday that as many as three U.S. missiles aimed at Iraqi targets may have landed in neighboring Iran.