Search the web for "Linux Malware" and you will find many articles of hacked Linux systems.
Here is a recent one:
New HiddenWasp malware found targeting Linux systems | ZDNet
The National Vulnerability Database run by the US government lists over 7,000 vulnerabilities in Linux.
NVD - Results
Not all of these vulnerabilities have been found in the wild, but almost all of them were found by successfully hacking a Linux system, hopefully by someone wearing a white hat.