Wrong data receiving in my Arduino by bluetooth
Well, after a lot of research, it seems that my main problem was that I´m receiving and sending information at the same time. And with the library Softwareserial, only 1 can be active at the same time.
I found two solutions, but to be honest I'm not complete satisfy with neither of them. However, for my application will work.
The first solution: Is to used the HardwareSerial (pin 0,1) itself, instead of using the pin 2 and 3. When I used those, it didn't have any problem. Although I decided no to used because it help me debugging my code.
The second solution: Is to decrease the frecuency of what I´m sending. For me its ok I send the data every second. So my code would be like this:
#include &lt;SoftwareSerial.h&gt;
#include &lt;TimerOne.h&gt;
SoftwareSerial hc06(2,3);

char command;
String string;
boolean ledon = false;
const byte MAX_STRING_LEN = 40; 
const int  BLINK_INTERVAL = 1000;

char inputString[MAX_STRING_LEN];  // a string to hold incoming data

int BatteryPin = A0;    // select the input pin for the potentiometer
int sensorValue = 0;  // variable to store the value coming from the sensor
float BatteryCar = 0;
int PercentageBatt = 0;
int intensidad = 0;
byte strLen   = 0;                 // current length of rec'd string

#define led 11
void setup()
{
  Serial.begin(9600);
  hc06.begin(9600);
  pinMode(led, OUTPUT);
  Timer1.initialize(1000000);
  Timer1.attachInterrupt( SendVoltage );
}
void loop()
{

  sensorValue = analogRead(BatteryPin);
  BatteryCar = sensorValue * (5.0 / 1023.0);
  if (hc06.available() == 0)
  {
    analogWrite(led, 0);
    delay (10);
  }
  while(hc06.available() &gt; 0)
  {
    command = ((byte)hc06.read());
    if((command == '\n') || (command == '\r'))
    {
      command =='\0';
      break;
    }
    else if (command == 'O')
      analogWrite(led, 255);
    else
      analogWrite(led, 0);
    delay(10);   
    Serial.println(command);
  } 
}

void SendVoltage ()
{

  PercentageBatt = (BatteryCar * 100)/4;
  hc06.println(PercentageBatt);
}

I have read about this library (AltSoftSerial), but I couldn't get it work. I have usde the pin 8 and 9, but nothing.