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i also found the chip become very hot
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That's actually alarming. I don't think, that it happens because you're using a particular pin as output. As a more likely reason, you may have shorted a pin that is driven as output (e.g. an unused pin) or the device is simply damaged.
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you mean the signal tap is unbelieveable
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I mean, that some pins may be unaccesible for SignalTap by it's nature. SignalTap uses existing IO buffers and registers. If these resources don't exist for a particular pin, SignalTap can't work. There are some cases, where SignalTap can't access a pin (e.g. withh DDIO function) or doesn't necessarily reflect the pin state correctly (e.g. input function of bidirectional pins, but only in some cases, depending on other design parameters). I would expect problems also with dedicated clock outputs, but I'm not sure about.
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