This is likely due to improper drying of the wood fuel, if used moist or even wet wood produces a very large amount of smoke along with a fizzing/popping sound and this can result in buildup of soot in the chimney or even the spitting of super-heated steam.
The wood itself needs to be seasoned (Left to dry for 2 years to remove all the moisture in the wood) or alternatively the wood needs to be kiln dried to remove the moisture, the temperature in the stove needs to be hot enough to ensure
The main cause of a small area being blackened is when the log is positioned against the glass door, a large area is slightly more complex and could be due to the wood again being too moist
Wood used in solid fuel stoves should have less than a 20% water content otherwise a significant quantity of the heat produced is wasted boiling the water thus causing the wood to burn slow and cold.
This issue occurs because there is not enough heat being produced, refer to the manual on how to light the fire properly.
You should start by using paper and/or firelighters plus lots of kindling working up to larger pieces of wood until a good fire is established in the stove, attempts to start off straight with wood are met with failure.
It is possible that the stove might be running too cold if hard to remove black marks are appearing, nevertheless they can be removed by running your stove with full airwash enabled for 30 minutes to one hour or alternatively the use of Stovax spray cleaner for slight to moderate marks and the stovax gel cleaner for exceptionally stubborn marks.
Stained glass is a bit different as you cannot use any cleaners with a high acid or alkali content for risk of damaging the printing or even run the risk of removing it entirely by accident, a pH neutral glass cleaner like stovax spray cleaner would be the best solution as it is non damaging, softer and non corrosive.
To prevent this happening again make sure to only burn high quality low moisture wood at a high enough temperature to ensure complete combustion.
Over a period of time the fire cement holding the flue pipe in place may dislodge and fall down, normally this is caused by the heat from the stove which makes the pipe expand contract causing the cement to fall off.
Fortunately it is easily rectified by the application of additional fire cement which can be purchased from the shop for the price of £4.99/500g however this is not covered under warranty