1) can builder repay the entire amount without my sign & permission(cheque was given on joint name & my wife used joint account to withdraw the money)?
She might have played fraud with the builder too on the basis of which the builder in a blind faith settled the amount by making payment in the joint names. ow you should realise the fact that by mere marriage a husband and wife can maintain the joint living or habitation in all aspects. Except for procreation there is no necessity to have a joint venture in all the aspects, especially the assets whether movable or immovable. What was the necessity to have a joint bank account and why do you still operate the joint account? even now you can write bank requesting for closure of joint account as you are not willing to operate the joint account anymore owing to the pending matrimonial disputes.
2) to avoid the same problem for other property , can I make injunction application for navi Mumbai property in Bandra family court?
In another property you have only half share in it hence you may file a partition suit and also seek injunction restraining her from alienating the property in the same family court.