AIX process finish ok, but when I check the text file, inside it, I see this rarely character: ^M

Experts,

I have a problem with a text file integrity

1_an AIX process finish ok, but when I check the text file, inside it, I see this rarely character:   ^M

2_it is in pdf file: Error - The number of lines in the file does not match the amount reported on Trailer

3_why is different the structure in  the file below?

Evidence:

before the process:

MOA60 000000000274987,20ARS20131017

SEQ     120131017   169000000000184987,20ARS

RFFCR 242019310170039

RFFCK 0056045338

MOA11 000000000184987,20ARS

MOA9  000000000184987,20ARS

SEQ     220131017   169000000000090000,00ARS

RFFCR 009037310170079

RFFAIK009037310170079

MOA9  000000000090000,00ARS

TRL    202693093

after the process:

LIN     1   20131017                           ^M

MOA60 000000000274987,20ARS20131017^M

SEQ     120131017   169000000000184987,20ARS^M

RFFCR 242019310170039                    ^M

RFFCK 0056045338                         ^M

MOA11 000000000184987,20ARS^M