There are issues whenever you try to share an SD card with another SPI device. Some work arounds work most of the time, but what works all of the time is to put the SD card on its own SPI bus with dedicated SCK. I've done this with Moteino Mega without any problems.
Alternative is to not use any other SPI device when you're using the SD card. That is, Init SD, open file, do file io, close file, flush SD, and uninit SD. Then do any other SPI devices.