As pointed out, unless there is a precalculated md5 of the file published at the remote end that you can compare your locally calculated value against, calculating an md5 locally doesn't buy you anything.

For a simplistic check, but one that will detect common errors like ascii-v-binary tranfers and partial transfers, use the size method of NET::Ftp to get the remote size of the file and compare that against the local size after transfer. It won't detect in-transit corruption nor deliberate replacements, but then neither will a local MD5 without something reliable to compare against.