You're likely watering too often... but what kind of trees do you have? Where do you keep them - indoors or out? In the sun? Where do you live climate-wise? Bonsai is a technique used on any kind of tree, it is not the name of a particular tree though so not knowing that it's hard to comment otherwise. However, turning black usually means fungal problems which usually happen when conditions are too wet.

Thanks for the reply from seed I'm trying to grow English Oak, pomegranate and Chinese elm, they're indoor on a south faceing window cill I live in a seaside town on the northeast coast of England so it's often wet and windy,there has been small white patches of mould on the top of the soil is this an indication of a fungal problem thanks for your time,

Definitely fungus... but oak and elm are outdoor trees (full time) where you live so find a place to plant them, not in a bog or extra windy spot and with sun filtered through another tree (at least thru midday). They need the light but new transplants won't do that well in their first season 'out' in full sun all day. And let nature do the watering. Find the most sun for longest hours to keep the pom indoors in winter, but for now it could go out as well (until overnight temps go below 50). And maybe do some serious reading on taking care of it... water less often... at Bonsai4me.com, or other bonsai sites... and pom care in general.

Thanks for the info,will the fungas go if I just remove it or will I need to do something more?

3 of my plants

You can get an antifungal spray (or drench - as roots are probably affected by now) at a nursery or possibly hardware, but make sure it's for house plants vs large trees or veggies, etc... and follow directions.