I play the acoustic guitar (3 steel, 3 nylon) but whenever I use a plectrum it makes a scratchy sound, am I doing anything wrong or is it just me?
It is your plectrum technique - the edge of the plectrum is catching the string windings, but by looking to hold it more flat against the strings you will get less of it.
Note that you wont completely remove this sound as it is inherent when bits of plastic brushes against rough metal windings. I play with fingers a lot of the time, and as my thumbs and tips have got harder, this also produces a sound akin to scratching.
Once you hear something it can sometimes be diffcult to 'unhear' it. I suggest not listening too deeply because trying to pick out the nuances of the sound can lead you into trouble when you spend forever listening to one overtone that nobody else is bothered about.
'Time is money', as they say in the industry.
"I play the acoustic guitar (3 steel, 3 nylon)". I'm assuming you are using folk strings called "silk and steel", which means the top three strings are silver wound nylon and the bottom three are steel. They create a very mellow sound but don't last long as I use them myself for fingerpicking sometimes as they are ideal for recording. They are easier on my fingernails too as I don't like finger picks.
Try using a nylon pick and not plastic ("Dunlop" make them) and make sure it is a "medium" thickness and not "light". Light picks are very noisy in my personal experience with them.
You could also try what my wife uses, a "felt" pick ("Mahalo" brand). They are felt covered plastic or nylon and last a surprisingly long time. Very mellow sound and no pick noise whatsoever!