This is a bug in Cocoapods -And probably it won’t be fixed in a long while-
Running export COCOAPODS_DISABLE_DETERMINISTIC_UUIDS=YES on the Terminal seems to suppress the warnings for now.
EDIT Feb 2016:
In latest version of Cocoapods this has now been moved to the install section of the Podfile: install! 'cocoapods', :deterministic_uuids => false