Can weathering change the composition of something so that it appears different? There's a murder trial ongoing in Ireland at the moment and one of the pieces of evidence is a spade found at the scene along with the skeletal remains. It was contended by the prosecution that this spade was belonging to the defendant but while they were similar


  "forensic evidence found the paint splatters on the spade were not the
  same as on the [defendant's] garden fence"


My question is: can something left out in the open be changed either chemically or structurally by the environment such that it appears to be similar but not the same? If so why would this not have been called out as a caveat by the expert forensics witness?

The specifics of the chemical tests weren't gone into in the media (sample article here) so I don't know how accurate it was.
Yes, weather can and probably will change the composition of materials and make them different. 

However, forensic analysis usually takes that into account. There are some properties that might change because of weathering (you shouldn't compare water content, for example), but others won't. According to the sample article, the difference was found in the chemical composition of the paints.  Since details were not disclosed, one can only guess what these differences are, but some possibilites are:


Presence or absence of metals in the paints
Substances that wouldn't appear or disappear because of wheatering
Different isotopic ratios of elements
Traces of the solvent indicating they were not the same
Probably others


Assuming the analysis were performed correctly, it is usually not hard to say two samples are different. On the other side, when the results are similar, you can hardly say they are equal, but only that they match and that no differences were found.