I have heard some rumours about Lincoln's negative opinion about the Native Americans. Unfortunately, neither Wikipedia articles nor other Reddit posts couldn't enlighten me on this particular topic. Maybe I should have searched and read more carefully but I still would like to ask my question here in the hope you will help me.
A place you might start looking is the Dakota War of 1862 (Wikipedia Link). Years of escalating tensions between native Dakota Indians and white settlers in southwest Minnesota lead to several months of open conflict between the Indians and the settlers. When it ended more than 300 Dakota had been captured, tried in military trials and sentenced to death. Lincoln commuted the death sentence on most of them and December 26, 1862 38 Dakota men were hung in Mankato, Minnesota. It remains the largest mass-execution in US history. The 150th anniversary of the war was in 2012 and that prompted a lot of new articles and scholarship, a lot of it dealing with Lincoln's role in the executions so it should be fairly easy to find some things to get you started.
Also, Lincoln's grandfather was murdered by Natives in Kentucky.