You make sure that employees don't own what they write, but sign it over to the company (usually language to that effect in the employment contract, if there is none).

Also running tools like Black Duck over your source code tree to check open source license types or use of unlicensed code snippets from the Web.

NDAs can be given to people who know how something is done, knowledge that they could use to re-create the product or service elsewhere, which the acquired does not want. In some cases (that I have not personally seen) making people sign non-compete agreements, meaning if they quit they cannot work on the same thing for some time (not legal everywhere).

If "BigCorp" buys "CoolIdea" for their nifty piece of software "SecretSauce" they do not want to find out later that "BigCorp"/"CoolIdea" is required to publish source code for "SecretSauce" because it's based on "GNUOpenSauce" or that "CoolIdea" was selling something based on "FSFSauce."

Big companies are very allergic to GPL-like copyleft licenses. You generally have to go over the entire dependency tree with a fine tooth comb and make sure that nothing is going to get you sued to released the source code (inside a big company there are processes to ensure this on an ongoing basis)