It happens surprisingly frequently, although we take it for granted that the census records we routinely use (except for 1841) are headed by the 'head'.
But here are some exceptions.
Perhaps the best known example comes from the 1851 Census of St George Hanover Square.
The enumerator has potentially had to think on his feet here. How can the Queen be head of the household when she is a woman with a husband at home on the evening of 30 March 1851? To get around the problem, the Queen has been listed first as 'wife' and Prince Albert second as 'head'.
The form and instructions for 1851 (available at histpop) clearly state:
The assumption being that the Head is generally expected to be a married man.
Difficulties also sometimes arise at grand houses. There are few grander than Chatsworth House in Derbyshire, for example. On the night of 2 April 1911 the family weren't there, and the first name on the schedule is Ann Young, the housekeeper. She lists herself, and an entire schedule full of maids and porters as 'Servant', avoiding the need to list herself as Head of the 140 room household. (See 1911 Census; Chatsworth Edensor, Derbyshire, ED 20, SN 58). The enumerator filled out the other side of the schedule saying that the Head of Family is 'His Grace the Duke of Devonshire'.
At the Stables nearby, Reuben Clarke has listed himself first on the schedule, but refrains from providing any relationships at all. Again, on the other side of the schedule, the enumerator names the Duke of Devonshire as the 'Head of Family or Separate Occupier'. (1911 Census; Chatsworth Edensor, Derbyshire; ED 20, SN59).
You don't need to be looking at servants in the biggest houses either. Closer to home, Margaret Walne was a kitchen maid at Coulthurst, Bashall Eaves in 1901. As in the 1851 case above, we're looking at the enumeration books rather than the original schedule so we don't know exactly what the household recorded there, but we find another slight oddity:
Lady Holker appears in brackets with no further details. My suspicion is that she was not actually there that night, but the enumerator again didn't want to list the housekeeper as head of the household.
This is useful information for a researcher to have, but it's important to interpret it - depending on which site you use to search the census, sometimes she is indexed as being there, and sometimes she is not. It comes down to that old chestnut - check the original record!