I'm trying to calculate the internal resistance of my rechargeable batteries and haven't got a single battery holder so using I am having to using Banana plugs and Crocodile clips for holding my resistor. Then holding the banana clip on the negative end of my battery and reading the current. But could this be affecting my readings as I've tried different resistors and I'm still out in my calculation first time i got ~1000(with a 10k load) ohm now down to 10 ohm(with 68 ohm load). I have even smaller loads to test with now 1 ohm and 0.1 ohm. But this just popped in to my head as it might be problem. The leads I'm using are what we normally use for connecting our PCBs to the PSU, this is why I thought it could be ignored but maybe not when trying to calculate some thing very accurately.
No, it cannot be ignored.
The internal resistance of Lithium ion/NiMh batteries is comparable to one of the wires. Also you should keep in mind that a significant part of the resistance is in the connections to the battery.
So, for precise measurement, you can go for 4-wire measurement, or accurately measure the resistance of the wires and connections, and subtract it.