If you kept the plants long time in the tubes or magenta boxes,high concentration of salt, low concentration of calcium, low light, gas exchange. These are probably cause Vitrification.

A number of factors are involved .Stress causing metabolic disturbances is believed to be the major factor. Higher sucrose conc., ionic strength, high ammonium conc., high relative humidity, accumulation of gases (ethylene), hypoxia inside culture vessels, conc. of gelling agent etc. may lead to hyperhydricity or vitrification.

Density of tissue more than the capacity of vessel size vs medium volume.

Agar concentration is low

No gaseous exchange

The existing of vitrified tissue of previous cycle

Increase inositol level

Here's a list I compiled (and its not complete) of possible causes of hyperhydricity:

•Liquid media

•Chlorine ions

•Auxin imbalance

•Cytokini imbalance

•Other growth regulators

•Excessive NH4+

•Matric water potential

•Relative humidity

•Poor water pressure gradient between leaf and atmosphere

•Agar concentration

•Agar brand

•Choice of gelling agent

•Explant position on the media

•Ca+ and other ion or salt concentration

•Ventilation

•Temperature

•PPF

•Oxidative stress

The most common cause in my opinion is high humidity in the vessel. 

Hi

The reasons for the occurrence of vitrification in tissue culture plants is not clear. Several hypotheses have been offered to explain the cause of this physiological defect including high levels of cytokinis, low concentration of gelling agents, liquid medium and excess mineral elements. Various measures were found to reduce vitrification: increased carbohydrate levels in the medium, changed light intensity, modified concentration of agar, reduced humidity within the culture container. Vitrification is a complex phenomen depending on several chemical and physical factors acting together. The availability of water appears to be the central causal link.

http://agris.fao.org/agris-search/search.do?recordID=EE2001000311