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I am attempting to script diff and patch commands. Facing some warning like this if bzcat is used

# bzcat consolidated.patch.tar.bz2 | patch -d dev -p1 
  patch unexpectedly ends in middle of line
  patch unexpectedly ends in middle of line
# echo $?
  0

It there is no such warnings if patch is performed with decompressed file

# tar -xf consolidated.patch.tar.bz2
# patch -d dev -p1 < consolidated.patch
# echo $?
  0

I did compare resultant folder but both approach but they are identical

# diff -aurN dev1 dev2 > res.diff
# stat res.diff 
  File: res.diff
  Size: 0           Blocks: 0          IO Block: 4096   regular empty file
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Based on the filename, and the fact that it opens with tar, your consolidated.patch.tar.bz2 is a tar archive that has been compressed with bzip2. It's not like a zip archive where a single tool handles both sticking the files together and compressing them, but the two steps of aggregating the files (tar) and compressing the lot (bzip2) are distinct. (Except that smart implementations of tar know the common compression tools and can execute them automatically.)

So, what you get with bzcat is not the file(s) archived within, but the uncompressed tar archive. Even if it only contains one file. No wonder patch can't read it.

With GNU tar (at least), you could use the -O/--to-stdout option to have the file data sent to stdout:

tar -xj -f consolidated.patch.tar.bz2 -O | patch

(Or, ... -O consolidated.patch to output only that file, in case it wasn't the only one after all.)

With only a single file, there wouldn't really be need for the tar step, and the file could be compressed without using tar, just with bzip2 consolidated.patch, creating consolidated.patch.bz2, which bzcat then does work on.

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