Google marks a website with this warning if they find any suspicious code that could be a malware or trojan. Sometimes the reason for this is that your website is hacked and is now used to distribute malicious code.
Another common reason for this error is showing ads from low quality advertising networks.
Sometimes even when you clean your site thoroughly, the malicious code can keep coming back until you find and remove the backdoor placed on your site. Once you have successfully removed the backdoor, you will still need to thoroughly check all your files and database for any malicious code.
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