Have you played a chord near the head stock of the guitar then play the same chord in a position further down the neck? We all do as this is part of playing. Are the two similar frequency chords in tune with each other? NO? Well, this could be due to a number of issues due to normal play wear or simply an intonation adjustment. The first five frets usually have the greatest amount of wear but wear is not limited to this region alone. This example is a guitar that is in decent condition.
To conclude if the guitar frets are worn and eroded; pull your strings to the side and look for fret wear. Fret erosion usually look like this.
These indentations are a result of the string vibrating on the frets and thus eroding the fret wire. Strings are generally made of a harder material than the frets (except for Stainless Steel frets) and these marks will inevitably appear on your frets over a period time dependant on usage and technique. Here is a closer look at the fret erosion.
The effect the indentation has on the note being fretted is not welcome. The worn fret will allow the string to move closer to the fret board thus increasing the tension and making the note sharper than a note fretted on a unworn fret. These indentations or string erosion patterns can wreak havoc on intonation. In fact, setting string intonation on a guitar with worn frets is ineffective.
If you discover worn frets then you need to take your guitar to a Luthier. As long as the frets are not deeply eroded then your local luthier can file and level all the frets at a small cost that is usually approximately $100.00 US dollars. Do not try to simply level the frets in question. Doing so will only remove the erosion but the guitar will still not play in tune with itself. The guitar is a beast of burden and the more it is used the more maintenance it will require. If you play with this aforementioned situation you will find that the guitar will not play "in tune" throughout a scale and will not maintain "tune" through multiple chord positions.
If the guitar does not have string erosion but still will not play scales or multi-position chords in tune, then it may simply need an intonation adjustment. An intonation adjustment is where single string saddles are moved to increase or decrease the effective string length to make the given note play sharp or flat as required. Bring the guitar to a shop for repair. This is a non invasive repair that dependent on the shop work backlog can be repaired in usually an hour.
Lastly, changing the guitar string gauge, raising, or lowering the string height will create intonation problems. Unless you have great repair book, mechanical aptitude, and common sense then it is best to leave these adjustments to the pros. If you screw it up then the pro's will realize this quickly and you will probably receive an increased fee to untangle the mess created on the instrument.
The only work around for fret wear is not acceptable because it requires that you stop playing the guitar!! Besides, fret wear is a badge of honor as only those who practice and play receive fret wear. Stay home and practice or stay home!!!