Which shortcuts? Please be specific.
for example proportional scaling, cmd+shift and alt+shift. Same as illustrator..Also when I use Line tool holding shift..
Do you have any Chrome extension installed like LastPass or do you have Webroot installed in your machine, if yes, please remove it and then restart InDesign and check.
You should also try to reset the preferences of InDesign in case of no.
Please see : InDesign CC Shortcuts - Chrome - LastPass - YouTube
In order to reset preferences, you need to (Mac OS) While pressing Shift+Option+Command+Control, start InDesign. Click Yes when asked if you want to delete preference files.
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I did try everything and nothing worked but I talked to our IT guys and they said that the problem was with the anti virus program:
Secure Keyboard Entry on OSX interferes with keyboard shortcuts in InDesign CC 2015.
Disabling that function restores keyboard shortcuts
Everything is working fine now!