How can electromagnetic interference from a USB charger cause a capacitive touchscreen to malfunction?
Touch screens have transmit (Tx) and receive (Rx) electrodes which are drawn in transparent indium tin oxide (ITO), forming a matrix of crossed traces with each Tx-Rx junction having a characteristic capacitance.  The human finger is basically a ground that alters the mutual capacitance between the RX and TX electrodes.  This network is very sensitive to changes in charge (i.e. capacitance changes).

Typical chargers use a flyback circuit topology. The interference waveform they generate is complex and varies considerably between chargers, depending on circuit details and output voltage control strategy. The interference amplitude varies considerably depending on how much design effort and unit cost the manufacturer has allocated to shielding in the switching transformer. 

Typical EMI parameters making this interference hard to filter include:


Wave shape is complex, consisting of pulse-width modulation square wave
followed by LC ringing 
Frequency rates 40–150 kHz under nominal load, with pulse-frequency or skip-cycle operation dropping frequency to &lt; 2 kHz when very lightly loaded
Voltage levels up to one half input peak voltage = Vrms / sqrt(2)


These interference voltages are coupled capacitively from sources that are both internal and external to the touchscreen device. These interference voltages cause charge movement within the touchscreen, which may be confused with the measured charge movement due to a finger touch on the screen.

This form of EMI has many coupling paths which can disrupt the TX/RX electrode capacitance measurements:  internal (poor shielding in device), external parasitic (finger-device introduces closed ground loops, etc).  Poorly designed chargers or poorly shielded devices (or both) can exhibit touch screen problems.