Can't use two SPI devices at the same time
The LedControl doesn't use SPI library but it's using shiftOut internally. So you can't use them both at the same pins as the SPI interface takes over them.

Basically SPI.begin() takes over the control on its pins and that means when you use digitalWrite or pinMode on those pins, it'll be ignored (at least on some of them).

If you add SPI.begin() into the second example (LedControl one) it'll stop working. However you can change pins for LedControl to other (free) pins and it should be working again.

And also there are mixed signals between both devices:

HW SPI wiring:
13  CLK    output
12  MISO   input
11  MOSI   output
9   SS     output

and LedControl wiring is:
12  MOSI   output (not really)
11  CLK    output


Something from the datasheet about alternate pin functions:


  
  SCK/PCINT5 – Port B, Bit 5
  SCK: Master Clock output, Slave Clock input pin for SPI channel. When the SPI is enabled as a
  Slave, this pin is configured as an input regardless of the setting of DDB5. When the SPI is
  enabled as a Master, the data direction of this pin is controlled by DDB5. When the pin is forced
  by the SPI to be an input, the pull-up can still be controlled by the PORTB5 bit.
  PCINT5: Pin Change Interrupt source 5. The PB5 pin can serve as an external interrupt source.
  MISO/PCINT4 – Port B, Bit 4
  MISO: Master Data input, Slave Data output pin for SPI channel. When the SPI is enabled as a
  Master, this pin is configured as an input regardless of the setting of DDB4. When the SPI is
  enabled as a Slave, the data direction of this pin is controlled by DDB4. When the pin is forced
  by the SPI to be an input, the pull-up can still be controlled by the PORTB4 bit.
  PCINT4: Pin Change Interrupt source 4. The PB4 pin can serve as an external interrupt source.
  MOSI/OC2/PCINT3 – Port B, Bit 3
  MOSI: SPI Master Data output, Slave Data input for SPI channel. When the SPI is enabled as a
  Slave, this pin is configured as an input regardless of the setting of DDB3. When the SPI is
  enabled as a Master, the data direction of this pin is controlled by DDB3. When the pin is forced
  by the SPI to be an input, the pull-up can still be controlled by the PORTB3 bit.
  OC2, Output Compare Match Output: The PB3 pin can serve as an external output for the
  Timer/Counter2 Compare Match. The PB3 pin has to be configured as an output (DDB3 set
  (one)) to serve this function. The OC2 pin is also the output pin for the PWM mode timer
  function.
  PCINT3: Pin Change Interrupt source 3. The PB3 pin can serve as an external interrupt source.
  SS/OC1B/PCINT2 – Port B, Bit 2
  SS: Slave Select input. When the SPI is enabled as a Slave, this pin is configured as an input
  regardless of the setting of DDB2. As a Slave, the SPI is activated when this pin is driven low.
  When the SPI is enabled as a Master, the data direction of this pin is controlled by DDB2. When
  the pin is forced by the SPI to be an input, the pull-up can still be controlled by the PORTB2 bit.
  OC1B, Output Compare Match output: The PB2 pin can serve as an external output for the
  Timer/Counter1 Compare Match B. The PB2 pin has to be configured as an output (DDB2 set
  (one)) to serve this function. The OC1B pin is also the output pin for the PWM mode timer
  function.
  PCINT2: Pin Change Interrupt source 2. The PB2 pin can serve as an external interrupt source.