Best practices to avoid having legit program being flagged by virus scanners?

[cdevidal]

I'm creating an app for SecureCoop.com, no malware, but Microsoft antivirus keeps flagging my installer as malware. First Trojan:Win32/Wacatac.B!ml then Backdoor:Win32/Bladabindi!ml.

I can't be unnecessarily scaring my users. What are the best practices to avoid this happening?