There most certainly is machlokes. Some matters are by already decided by the Rabbeim, etc., but some are a machlokes about what the Rabbeim decided, some are decided by well respected Rabbanim within Chabad (like Rabbi Avraham Chaim Naeh) and some are just a question for a Rav, not having a previous answer, or that are heavily dependent on circumstances.
Most Halachic questions that people wrote to the Rebbe, he would tell them to ask their own Rav. I remember a speech by a Rav in Israel where he was at a gathering of Rabbanim in Israel and he mentioned that the Lubavitcher Rebbe had told someone to ask a Rav the question she had sent him. Then throughout the room, the different town Rabbanim started saying they had the same experience.
Obviously, all of these Rabbanim have different opinions, and do not pasken monolithicly, but the Rebbe sent people to them. (Lubavitchers prefer Lubavitcher Rabbanim for their psak because it will reflect the derech of the Alter Rebbe, the Tzemach Tzedek, etc. - The Rebbe never specified a specific Rav, though).
Just one example - can you Kasher a self cleaning oven with a self cleaning cycle or two, or is the cleaning cycle not good enough? Just within Crown Heights this is a disagreement between the different Rabbanim that have been on the Beis Din. So, not everyone has the same practice.
Ephraim points to an even more intricate one, which speaks to a "what does the Rebbe hold" type of question.
First some background. It is a fairly well known Machlokes Achronim if a Ben Eretz Yisroel that travels to Chutz L'Aretz or vis-versa keeps Yom Tov like the local community or like the community that he came from. Generally, most poskim that people are familiar with hold of some level of 2nd day Yom Tov in Eretz Yisroel if they are returning (especially if they are not there with their wives), but some (most famously the Chacham Tzvi) don't, they hold it is all dependent upon the location where you spend Yom Tov.
From the second edition of Shulchan Aruch HaRav, it seems that he holds like the Chacham Tzvi. The Shar HaKollel* specifically writes this. However, the Lubavitcher Rebbe in the early years pointed to specific instructions from the Previous Rebbe that two days should be kept, this overrides any interpretations of the Alter Rebbe (this was regarding a group traveling for Pesach, those with their wives kept one day but no Chametz on the 8th day, Bochurim away from their family two days). This is in writing and published in a letter.
Subsequently, there are records of the Rebbe saying things that may or may not be consistent with this (it is not clear), primarily printed in a sefer called המלך בסיבו, a collection of written memories of discussions at the Lubavitcher Rebbe's Shabbos or Yom Tov meals.
There are some Rabbonim who look at this and say that the Rebbe changed his opinion to be that of the Chacham Tzvi. Others find the evidence of that way too thin. So there is no clear Chabad practice in this area, everyone follows their own Rav.
*Sorry for the French link, but I could not find one in English