When the letter is delivered to the cottage, Withnail picks it up from the table to read it. In the following shot, he is holding the envelope at the back of the letter which wasn't in his hands in the previous shot.
A road sign for the M25 London orbital motorway can be seen at one point as Withnail and Marwood are driving along the motorway on the way back from the cottage. This was road was constructed in the 1980s, well after 1969, the year in which the film was set. The folded metal crash barrier is a thing of the late '70s at the earliest. Numerous cars dating from the 1980s are seen on the motorway.
The word "Provos" can be seen on the wall of the pub as Withnail and Marwood leave, however the Provisional IRA were only formed in December 1969 which is at least a couple of months after the film is set.
When Withnail and Marwood run out of the Mother Black Cap pub, Trellick Tower is visible in the background (in the DVD commentary Bruce Robinson talks about he hated this building) but it wasn't completed until 1972, this film is set in 1969.
When Marwood is seen knocking at the Penrith cottage door looking for the farmer, there is a distinctive black coal bucket outside. When the camera pans out before he leaves, the coal bucket is no longer there.
When Withnail and Marwood are driving along the motorway on the way to the cottage, at least one motorway construction vehicle can be seen driving in the same direction, but on the other carriageway. This gives away the fact that the motorway scenes were filmed on a completed but as yet unopened section of the M25 motorway.