If you use third-party source control tools, you must register your model file extensions (.mdl and .slx) as binary formats. If you do not, these third-party tools can corrupt your model files when you submit them, by changing end-of-line characters, expanding tokens, substituting keywords, or attempting to automerge. Corruption can occur whether you use the source control tools outside of Simulink® or if you try submitting files from Simulink Project without first registering your file formats.
Also check that other file extensions are registered as binary to avoid corruption at check-in for files such as .mat, .mdlp, .slxp, .sldd, .p, MEX-files, .xlsx, .jpg, .pdf, .docx, etc.
For instructions with SVN, see Register Model Files with Subversion. You must register model files if you use SVN, including the Built-In SVN Integration provided by Simulink Project.
For instructions with Git, see Register Model Files with Git.