Okay, there are a couple of issues.
The strange numbers for negative temperatures are caused by (2) issues.
1. The LCDOUT commands are being used with the DEC modifier.
This will not always output the same number of characters and may leave previously printed characters on the screen.
It will depend on the value to be displayed.
Use the DEC2 modifier instead. This will force the output to always be (2) characters.
Since th DS3231 only has a temperature range of -40 to +85, this will be fine.

2. The DS3231 only uses a simple bit <b7> to indicate the sign. It does not really encode to 2s compliment.
Adjusted the test and handling of negative values below.

See if this works for you now.

Code:
''You really should not use constants for the address parameter for I2CREAD & I2CWRITE
'' From the PBP Manual
''Constants should not be used for the Address as the size can vary dependent on the size of the constant. 
''Also, expressions should not be used as they can cause an improper Address size to be sent.

''TempRegister CON $11      'temperature integer  REGISTER
''TempRegisterFRA CON $12   'temperature fraction REGISTER


TempRegister var byte    ' variable to hold DS3231 register address to read/write
       
       
TempInt var byte            ' Variable for temperature integer from register 11h
TempFrac var byte           ' Variable for temperature fraction for register 12h
TempSign var bit            ' Variable to hold sign bit   


main: 

LCDOut $fe,1

       B0 = 0
       button Taster0, 0, 100, 10, B0, 1, meni0


           
       I2CRead SDA, SCL, RTC, SecReg, [sec,MINs,hr,day,date,mon,yr] 


        LCDOut $fe,2,     HEX2 hr, ":", HEX2 MINs, ":", HEX2 sec 
        LCDOut $fe,$c0, HEX2 date, "/", HEX2 mon, "/","20" ,HEX2 yr
        
        
        
       TempRegister = $11h      ' DS3231 Temperature REgister High Byte (Integer portion)     
       I2Cread SDA, SCL, rtc, TempRegister, [TempInt, TempFrac]
       
       TempFrac = (TempFrac >> 6)   ' Shift <b7:b6> to <b1:b0>
       TempFrac = (TempFrac * 25)   ' Fractional portion is in .25 increments. Increment values are 0-3 (.00, .25, .50, .75)
       
       
       
       TempSign = TempInt.7   ' save the sign bit for later

       '''If TempSign = 1 then  TempInt = (TempInt XOR $FF) + 1     'Do not use this, the DS3231 uses simple <b7> sign with <b6:b0> as absolute temperature value
 



       If TempSign = 0 then     ' Positive temperature
           LCDOUT $FE, $80+9,   "+", DEC2 TempInt, ".",DEC2 TempFrac    'Change to DEC2 to make sure LCD does not leave characters from previous temperature printout
       Else                     ' Negative temperature
           TempInt.7 = 0   ' Clear <b7> and use only the absolute value of 11h register value <b6:b0>
           LCDOUT $FE, $80+9,   "-", DEC2 TempInt, ".",DEC2 TempFrac    'Change to DEC2 to make sure LCD does not leave characters from previous temperature printout
       Endif
         
       
    
       
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