The ^@s are most likely null characters in the file. You don't show us how $var gets its value so the nulls could be in the variable. My guess it that the printf to STDOUT isn't showing the nulls in your terminal window even though they are there, but whatever you are using to see the contents of the file is showing the nulls.
As a test you could pipe the output from your print version of the script to a file then inspect the file in the same way as you did for the script generated file. I expect you will find both files are the same and the problem is in how you generate the contents of $var.
Optimising for fewest key strokes only makes sense transmitting to Pluto or beyond
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