1. Using excess force. On the piano you have to strike the keys with more force in order to play louder. On the organ, the dynamics are done with the swell pedal, crescendo pedal, or employing different registration. Using too much force will damage the clarity of the piece that you play. Instead, always play mezzo piano regardless of the dynamic level of the composition.
2. Lifting your fingers off the keyboard. Pianists prepare each strike of the key with lifting the finger off the keyboard and driving it down. On the organ, you must use different muscle groups and whenever possible stay in contact with the keys. Lifting your fingers high in the air is not good for playing polyphonic organ music. Instead, always slide from one key to another (this advice is valid for pedal playing as well).
3. Imprecise releases. Because piano sound fades as soon as the key is struck, many average pianists are not aware of its ending (with the exception of the best ones). When such pianist tries to play the organ, he or she may depress the keys together (which is good) but will not notice or forget to notice the release of the note. Instead, try to be very precise by practicing in extremely slow tempo and especially separate parts and part combinations which will help you to control both the attack and release much better.
It doesn't matter what is your experience with the organ playing (several months or many years), the old pianistic habits will not go away unless you mindfully try to produce the sound differently on the organ and on the piano practicing organ music. Especially on the piano.
Here's the biggest danger of all - practicing organ pieces on the piano but with pianistic touch (because playing with organistic technique sounds strange and lifeless on the piano). Beware of this, switch to the organ playing mode and with every day practice you will develop a solid organ technique.