SD Card reading non existent files

Hello. I am working on a project that involves an Ultra Sonic sensor and the Adafruit Music Maker MP3 Shield. I have code working to trigger audio playback from stored files on an SD card, but there is an issue where the code is reading files that don't exist, and at times is calling these files for playback and nothing is happening.

I have tried to take things back a step and use basic Arduino code to read an SD card and list the files.

/*
  Listfiles

  This example shows how print out the files in a
  directory on a SD card

  The circuit:
   SD card attached to SPI bus as follows:
 ** MOSI - pin 11
 ** MISO - pin 12
 ** CLK - pin 13
 ** CS - pin 4 (for MKRZero SD: SDCARD_SS_PIN)

  created   Nov 2010
  by David A. Mellis
  modified 9 Apr 2012
  by Tom Igoe
  modified 2 Feb 2014
  by Scott Fitzgerald

  This example code is in the public domain.

*/
#include <SPI.h>
#include <SD.h>

File root;

void setup() {
  // Open serial communications and wait for port to open:
  Serial.begin(9600);
  while (!Serial) {
    ; // wait for serial port to connect. Needed for native USB port only
  }

  Serial.print("Initializing SD card...");

  if (!SD.begin(4)) {
    Serial.println("initialization failed!");
    while (1);
  }
  Serial.println("initialization done.");

  root = SD.open("/");

  printDirectory(root, 0);

  Serial.println("done!");
}

void loop() {
  // nothing happens after setup finishes.
}

void printDirectory(File dir, int numTabs) {
  while (true) {

    File entry =  dir.openNextFile();
    if (! entry) {
      // no more files
      break;
    }
    for (uint8_t i = 0; i < numTabs; i++) {
      Serial.print('\t');
    }
    Serial.print(entry.name());
    if (entry.isDirectory()) {
      Serial.println("/");
      printDirectory(entry, numTabs + 1);
    } else {
      // files have sizes, directories do not
      Serial.print("\t\t");
      Serial.println(entry.size(), DEC);
    }
    entry.close();
  }
}

And my serial monitor is looking like this..

Initializing SD card...initialization done.
SPOTLI~1/
	STORE-V2/
		00A22E~1/
			PSID.DB		8192
			TM~1.LIO		0
			LIO~1.CRE		0
			TMP.CAB		0
			CA~1.CRE		0
			INDEXS~1		28
			~1.IND		4096
			~~2.IND		16
			~~~3.IND		8
			~~~~4.IND		3277
			~~~~~5.IND		4096
			~~~~~~31.IND		440
			~~~~~~34.IND		4096
			~~~~~~37.IND		440
			~~~~~~40.IND		2056
			~~~~~~43.IND		8
			~~~~~~46.IND		1088
			~~~~~~48.IND		13
			~1.DIR		65536
			LIVE~1.IND		4096
			LIVE~~2.IND		32768
			LIVE~~~3.IND		16384
			LIVE~~~4.IND		3277
			LIVE~~~5.IND		4096
			LIVE~~69.IND		8192
			LIVE~~72.IND		4096
			LIVE~~75.IND		8192
			LIVE~~78.IND		8224
			LIVE~~81.IND		1024
			LIVE~~85.IND		65536
			LIVE~~88.IND		6519
			LIVE~1.DIR		65536
			STORE.DB		118784
			STOR~1.DB		118784
			REVERS~1		65536
			TMPSPO~1.STA		4096
			STORE_~1		4
			JOURNA~1.COR/
			JOURNA~1.LIV/
			JOURNA~2.LIV/
			JOURNA~3.LIV/
			JOURNA~4.LIV/
			JOURNA~1.ASS/
			JOURNA~2.ASS/
			JOURNA~1.HEA/
			JOURNA~1.MIG/
			JOURNA~2.MIG/
			JOURNA~1		0
			JOURNA~1.SCA/
			SHUTDO~1		4
			JOURNA~1.2		140
			REVERS~1.SHA		3136
			~1.SHA		4096
			STOR~1.UPD		12
			0DIREC~1.SHA		1088
			~~~~~174.SHA		2
			LIVE~1.SHA		4096
			LIVE~~2.SHA		464
			LIVE~~~3.SHA		0
			LIVE~~~4.SHA		8
			LIVE~~~5.SHA		2056
			LIVE~195.SHA		65536
			LIVE0D~1.SHA		1088
			LIVE~202.SHA		3
			REVERS~1.UPD		2
			TMPSPO~1.LOC		4190
	VOLUME~1.PLI		4315
FSEVEN~1/
	FSEVEN~1		36
	000000~1		230
	000000~2		71
TRACK001.AAC		25248
_TRACK~1.AAC		4096
TRACK002.AAC		32086
_TRACK~2.AAC		4096
TRACK003.AAC		26826
_TRACK~3.AAC		4096
TRACK004.AAC		27878
_TRACK~4.AAC		4096
TRACK005.AAC		23933
_TRACK~5.AAC		4096
TRACK006.AAC		23933
_TRAC~33.AAC		4096
TRACK007.AAC		29719
_TRAC~37.AAC		4096
TRACK008.AAC		40239
_TRAC~41.AAC		4096
TRACK009.AAC		28404
_TRAC~45.AAC		4096
TRACK010.AAC		24722
_TRAC~49.AAC		4096
TRACK011.AAC		22618
_TRAC~53.AAC		4096
done!

The files are all named track001 and so on. I have reformatted the card using the suggested programme on the forum homepage here. You can see in the serial monitor that it is calling files that don't exist such as _TRACK~1.AAC. It seems to be making a duplicate of each sound file, and each one is tagged with a number of 4096, but I don't know what these numbers represent? I also don't know what the FSEVEN~1 represents and that is sometimes called for playback when the sensor is triggered.

I have tried moving the files into their own directory but it is making no difference. Does anyone know why this is happening? Is there a way to exclude these names from the "playlist"?

usually file names with ~ happens with filenames that are not 8.3

.