First of all, we should know the meaning and definition of shirk and then check that is it applied on prostration on karbala's sand. No shia worships the sand of karbala or the holy shrine of Imam Husain a.s. as it has proclaimed by the enemies. That is a white lie. Actually prostration on the sand of karbala is totally different to worship the sand or the holy Shrine of Karbala. Reverence is a different thing from worship, that is obvious for every one who has a common sense. In fact According to the Shi'ah Ja'fari fiqh – which is one of the five main schools of law in Islam – prostration must be performed on pure earth or what grows on it, provided that it is not eaten or worn. This includes dust, stone, sand and grass, provided that it is not a mineral. Prostration on paper is permitted, because it is made of a material which grows on earth, but not cloth or carpets.
The legal scholars of all the Sunni schools of law concur regarding the validity of prostration on earth and that which grows on it.
• Narrated Abu Sa'id al-Khudri: I saw Allah's Apostle prostrating in mud and water and saw the mark of mud on his forehead.

[Al-Bukhari, Sahih (English translation), vol. 1, book 12, no. 798; vol. 3, book 33, no. 244]

The Prophet (s) also used to have a Khumra on which he would put his forehead for prostration.

• Narrated Maymuna: Allah's Apostle used to pray on a Khumra.

[Al-Bukhari, Sahih (English translation), vol. 1, book 8, no. 378]
• According to al-Shawkani, a famous Sunni scholar, more than ten Companions of the Prophet (s) have narrated traditions mentioning his prostration on a Khumrah. And he lists all the Sunni sources recording these traditions which include Sahih Muslim, Sahih al-Tirmidhi, Sunan Abu Dawud, Sunan al-Nasa'i and many others.

[Al-Shawkani, Nayl al-Awtar , Chapter of Prostration on the Khumrah, vol. 2, p. 128]

So what is a khumrah?
• a small mat sufficient just for the face and the hands while prostrating during prayers.

[Al-Bukhari, Sahih (English translation), vol. 1, book 8, no. 376 (as explained by the translator in paranthesis)]

Now the question is that why shia keep mohr made from the sand of karbala?

The Shi'ah prefer to prostrate on the earth of Karbala because of the importance given to it by the Prophet (s) and the Imams from his Family (Ahl al-Bayt). After the martyrdom of Imam Husayn (a), his son Imam Zayn al-'Abidin (a) picked some up, declared it to be sacred dust, and kept it in a bag. The Imams (a) used to perform prostrations on it and make a tasbih out of it, and recited Allah's praises on it.
[Ibn Shahr Ashub, al-Manaqib, vol. 2, p. 251]

They also encouraged the Shi'ah to perform prostrations on them, with the understanding that it was not compulsory, but with a view to achieving greater recompense. The Imams (a) insisted that prostration before Allah must be on clean earth only and that it was preferable if it was performed on that earth of Karbala.

[al-Tusi, Misbah al-Mutahajjad, p. 511]
[al-Saduq, Man la yahduruhu'l faqih, vol. 1, p. 174]