PHP: Nested If condition confusion (Display error)

Doesn't look too wrong (although the many nested ifs will guarantee headaches when it comes to maintaining the code, but that's not your question).

Check these:

• The gray cell else case outputs nothing in the <td>, which might account for empty cells.
• Setting $cond = TRUE should probably be set one level above its current place, though I doubt that would make too much of a difference now.
• If the NAME of the staff in your array isn't in correct case, you obviously have to compare something like strtoupper($value) == strtoupper(...array...).
• Your Sun/Sat comparison seems odd; wouldn't that be more like == 'Sun' and == 'Sat'?

Besides those, it's hard to tell what might be wrong. You'd have to provide a complete array of your data, the wrong output and the desired output, otherwise it's impossible to see which values lead to which output.

Edit: And what's the initial assignment to $inidate via print_r supposed to mean? I guess you would want to have the same assignment as at the end of your main loop, the strftime business?

After all, this is an example of way too complex and thus error-prone code. Consider renaming variables to something meaningful, not $value, and extract methods instead of nesting too deep.

Edit 2: Perhaps I didn't make myself clear. This is the code after my suggestions. Is the output better now?

$inidate = "$y/$m/01"; //$y and $m chosen by user
$count=0; 
foreach ($staff as $key => $team) //row or use count on staff
{
    $j=0;
    echo "<tr><td>".($count+1).".</td><td>".$team."</td>";
    for ($i=0;$i<cal_days_in_month(CAL_GREGORIAN,$m,$y);$i++) //column
    {
        $cond = FALSE;
        while (($dome[$j]['DATEIN'] != "") && ($cond == FALSE))
        {
            if ($dome[$j]['DATEIN'] == $inidate)
            {
                if (strtoupper($team) == strtoupper($dome[$j]['NAME']))
                {
                    if ($dome[$j]['TIMEIN'] != "")
                    {
                        $cond = TRUE;
                        if (date("D",strtotime($getdate)) == 'Sun' || date("D",strtotime($getdate)) == 'Sat')
                        {   
                            //if late output time in yellow cell
                            if (strtotime($dome[$j]['TIMEIN']) > strtotime('09:10'))
                                echo "<td BGCOLOR='#ffff00'>".$dome[$j]['TIMEIN']."</td>";
                            else //output time normally
                                echo "<td>".$dome[$j]['TIMEIN']."</td>";
                        }
                        else //if its weekday outputs gray cell
                            echo "<td BGCOLOR='#525266'>".$dome[$j]['TIMEIN']."</td>";
                    }
                    else
                        echo "<td>AB</td>";
                }
            $j++;
            }
        }
        $inidate = strftime("%Y/%m/%d", strtotime("$inidate +1 day"));
        echo "</tr>";
    }
    $count++;
}

Edit 3: Ok, the code's more messed up than I originally thought. I PhpFiddled it to this, which works as expected (I suppose) for the given input. I didn't care about coloring or other trivial changes. Moreover, I won't point out the changes, you can see them if you compare this to your original code. And you should extract methods, as I pointed out before and as was done in the other answer. "Extract methods" refers to a refactoring term (http://refactoring.com/catalog/extractMethod.html) and is not a PHP function.

<?php
$month = "01";
$year = "2015";

$staff=array('STAFF A-Full Name',
             'STAFF B-Full Name',
             'STAFF C-Full Name');

$dome[]=array('NAME' => 'STAFF A-Full Name',
              'DATEIN' => '2015/01/01' ,
              'TIMEIN' => '09:02');
$dome[]=array('NAME' => 'STAFF A-Full Name',
              'DATEIN' => '2015/01/02',
              'TIMEIN' => '08:30');
$dome[]=array('NAME' => 'STAFF B-Full Name',
              'DATEIN' => '2015/01/01',
              'TIMEIN' => '08:43');
$dome[]=array('NAME' => 'Staff B-Full Name',
              'DATEIN' => '2015/01/03',
              'TIMEIN' => '09:11');

echo "<table>";
$countTeam = 0;
foreach ($staff as $key => $team) //row or use count on staff
{
    $inidate = "$year/$month/01"; //$year and $month chosen by user

    echo "<tr><td>".($countTeam + 1).".</td><td>".$team."</td>";
    for ($i = 0; $i < cal_days_in_month(CAL_GREGORIAN, $month, $year); $i++) //column
    {
        $found = false;

        foreach($dome as $domeKey => $staffAssignment){
            if($found){
                break;
            }

            if ($staffAssignment['DATEIN'] == $inidate)
            {
                if (strtoupper($team) == strtoupper($staffAssignment['NAME']))
                {
                    if ($staffAssignment['TIMEIN'] != "")
                    {
                        $found = true;
                        if (date("D", strtotime($inidate)) == 'Sun' || date("D", strtotime($inidate)) == 'Sat')
                        {   
                            //if late output time in yellow cell
                            if (strtotime($staffAssignment['TIMEIN']) > strtotime('09:10')){
                                echo "<td BGCOLOR='#ffff00'>".$staffAssignment['TIMEIN']."</td>";
                            }
                            else { //output time normally
                                echo "<td>".$staffAssignment['TIMEIN']."</td>";
                            }
                        }
                        else { //if its weekday outputs gray cell
                            echo "<td BGCOLOR='#525266'>".$staffAssignment['TIMEIN']."</td>";
                        }
                    }
                    else {
                        echo "<td>AB</td>";
                    }
                }
            }
        }

        if(!$found){
            echo "<td></td>";
        }       

        $inidate = strftime("%Y/%m/%d", strtotime("$inidate +1 day"));
    }

    $countTeam++;
    echo "</tr>";
}
echo "</table>";
?>