There are many reasons, some of these may not be true, alot are from a book I read:
One reason is due to the attiutde to their founder, some say that they treat him as a more important figure than the pope himself; apparently once an Opus Dei organisation/ group asked the vatican if they could celebrate easter later, due to the fact that the founder (Saint Jose Maria Escriva de Balaguer) had an anniversery - could have been his birth.
Another reason is due to the old practices some of the members still do, such as sprinkling holy water on the bed before sleeping in it and also the discipline (the minority do this).
One reason was due to the beatifcation and cannonization of Jose Maria Escriva de Balaguer. Two popes before JP2 had denied this honour, however JP2 did not deny it.
Some also say that it is because of the title the organisation holds - Personal Prelature. This group is answerable to nobody (except maybe the pope) it is the only organisation to ever have been given the rank. As well as this some say that they should not hold the rank as it was designed for missionaries in far out places that could not be contacted, not a world organisation. Opus dei members are answerable to very few, if they are in a diocese by a non opus dei bishop, then that bishop has no jursidiction over them.
Also the way that members are treated. There are many super numeraries of the group that donate entire salaries to the organisation, this is one way that Opus Dei were able to get the vatican bank out of the blue years back. Also women and men have to use diffenerent entrances to Opus Dei buildings.
What is more the secrecy of the organistaion is what causes some suspision, it is quite hard to become a member, and often you have to be approached by an existing member and asked to join.
There is also the nature of Jose Maria’s guide book, ‘Il Camino’ it has some strange philosophy in it like:
“Stay quite and you shall never regret it, speak and you often will”
Whats more the book containing all the information about Opus Dei, was forced by the pope to be produced (opus dei didn’t want to make it) it had to be given to every bishop that had opus dei parishoners in their diocese, it was often personally handed over, opus dei were very careful to make sure nobody else got it.
I am sure that these points will not apply in every Opus Dei place, and that the group is genuinely an organisation of love and God’s word. I think that there are some Opus Dei members on the forum?