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Welcome @rounakaungaug:
It's normal to perceive a neutral grey surrounded by blue as yellow.
It's called an optical illusion, but it's much more than that.
There are physical elements involved such as the interaction of light frequencies, physiological aspects of your color receptors, psychological aspects, and how the brain tries to correct perception in a contextual way.

As for customizing the buttons, I have good news for you.
It's possible through QSS.
Here you can find some QSS themes, you can start from them to learn how to customize Qtractor at a more detailed level than just the color:
https://sourceforge.net/projects/visualthemes-qtractor/

For example customize mute button:
qtractorTrackButton[text= "M"]:checked {
color: #ffff00;
background: #525234;
}