Deep colour coat

Is it normal for the deep colour coat to be patchy like this?,this is mahogany colour
http://www.pitbullguitars.com/wp-con.../2og49-012.JPG

How long did you sand the body of the guitars for?
did you work through the sandpaper grits sequentially, from 120 to 180 to 240 etc.
What grit did you finish with?
glue spots all removed if any?
Sweating over the body while sanding....

Usually the uneven ness is caused by certain parts of the body absorbing colour better than other parts.
If the body has not been sanded WITH the grain throughout you can get scratches across the body. If you havent sanded the body through the range of grits thoroughly your surface will not be consistently even.
If you didnt go fine enough the body is likely to absorb more colour than if you did.
Where all the glue spots removed? where there any over shiny spots caused by over sanding, i.e. Polishing the wood?
If you sweat on your guitar body while sanding it can darken the colour when applying it!

i started with 180 and then moved onto 240 removing the glue spots and just giving the guitar an overall smoother surface

How much time did you spend sanding?

i spent roughly 20 minutes on 180 and 25 on 240

SgJames maybe you needed to sand with an intermediate grit. The PBG sandpaper kits come with 180, 220 and 240 grit so you missed the 220 grit. You may be able to get some fine steel wool 0000 grade and really concentrate sanding the patchy areas once the wudtone has cured for at least 24 hours. Could be a number of reasons as Gav pointed out. You also need to do a last wipe with the rag when applying wudtone with the grain and look at the surface reflection looking for areas of wudtone that were'nt ragged properly ie blotches or any excess wudtone.
I typically spend up to 2 to 3 hours total sanding the body before any application. Also before you apply any wudtone rub a damp rag (water or turps) will show up any glue, machine marks, filler or shallow scratches. Hope this helps

Agree with Wokka.....also what you have here is a bass wood body which before you do the final sand you should rub the body with a damp cloth which gets all the fluffy fibres to stick out and which you can then cut when you do the final sanding. This also helps get the finish nice and smooth. I am not too concerned about you missing the 240 grit because i usually start with 120 if I find any deep scratches before moving onto 180 and finishing on 220. But the quality of sandpaper i am using probably assists me greatly in being able to do this. This is not to say anything negative about the sandpaper you may have used.