This would happen if a later object segment had a more restrictive alignment than previous object segments that contribute to the same load segment, as in the following example:
s1 start
jsl s2
rtl
end
align 256
s2 start
rtl
end
These alignment requirements can be satisfied by just giving the load segment the most restrictive alignment of any object segment (since all alignments are powers of 2) and inserting space as necessary to align the code from each object segment.