I have made a lot of truffles, and even more ganache for other purposes, and I have never had this happen. My guess is that you are boiling the cream too hard and that is causing the curdling.
How to make ganache:
You will need by weight one part 35% cream to 2 parts chocolate of your choice.
Chop your chocolate (if it's in blocks or chunks), put into a heatproof bowl (stainless steel is best) away fro your heat.
In a saucepan or pot (depending on how much you're making), bring the cream up to a high simmer.
Pour the cream immediately over the chocolate and stir with a silicone spatula if you have one, a wooden spoon otherwise. The chocolate should completely melt within about two minutes; longer for very high percentage dark chocolates. At this point if you are making flavoured truffles, add your flavourings (unless your flavour compounds have been infused into the cream).
Chill until set, make into truffles.
Edited to add:
If you are using alcohol as a flavouring in your truffles, you will need to use either more chocolate or less cream. I have found that approximately for every fluid ounce of alcohol added, remove 3/4-1 fluid ounce of cream from the recipe. I prefer to infuse flavourings in the cream, and have had great success with beets, bacon (with a Guinness reduction added to the chocolate later), black truffle and pureed walnut, and honey. Be sure to strain, of course, before adding the hot cream to the chocolate.
I have also found that white chocolate will often need slightly less cream than a milk or dark.
One thing you could do is reduce the amount of lemon juice, and add some lemon zest. This will give you much of the lemon aroma without so much acidity. Try adding some zest to the cooking and then grate a little more on the finished plates, just before serving. Use a microplane.
Best Answer
The cream and yoghurt will separate and curdle if you bring it up to a boil. If you cook the dish longer at a lower heat, you should be able to avoid this. Slow cooking will tend to make the chicken more tender as well.
You need to keep the temperature of the yogurt below 190F (88C) to avoid having the milk proteins (mostly casein) react with acidic ingredients in the recipe and curdle. The acid comes from the yogurt itself and the ginger-garlic paste (most commercial, prepared ginger-garlic pastes have citric acid or similar as a stabilizer). You need to cook the chicken (and marinade because of its contact with the chicken) thoroughly, until it gets to up to at least 165F for food safety, but you do not want the sauce to get to 190F or boil.
If you've made kadhi before (a curry from yoghurt thickened with chickpea flour), it is the same concept -- it will separate and curdle if you let it boil.
Likewise, if you're making paneer from milk you want to get it close to boiling so that it WILL form the protein bonds when you add acid in the form of lemon juice or vinegar.